Load genomic break data
Charles Plessy
13 October, 2023
Source:vignettes/LoadGenomicBreaks.Rmd
LoadGenomicBreaks.Rmd
knitr::opts_knit$set(verbose = TRUE, cache = TRUE)Introduction
This vignette loads the genomic breaks data, consolidates colinear
regions, extracts unaligned and unmapped regions, transfers annotation
data and saves the resulting objects in a serialised R object
(RData file) for reuse in other vignettes.
Related objects are stored in lists to avoid cluttering the environment.
Packages and data
suppressPackageStartupMessages({
library('GenomicBreaks')
library('ggplot2')
library("BreakpointsData")
})
genomes <- OikScrambling:::loadAllGenomes(compat = FALSE)## Warning in runHook(".onLoad", env, package.lib, package): input string
## 'Génoscope' cannot be translated from 'ANSI_X3.4-1968' to UTF-8, but is valid
## UTF-8
## Warning in runHook(".onLoad", env, package.lib, package): input string
## 'Génoscope' cannot be translated from 'ANSI_X3.4-1968' to UTF-8, but is valid
## UTF-8Genomic breaks
Long/short arm information
Short / long arm annotation will be done by the
GenomicBreaks::flagLongShort() function.
loadLongShort <- function(file, genome) {
file <- system.file(paste0("extdata/Annotations/", file), package = "BreakpointsData")
gr <- rtracklayer::import.gff3(file)
gr$source <- gr$type <- gr$score <- gr$phase <- NULL
GRanges(gr, seqinfo = seqinfo(getBSgenome(genome)), strand = "*")
}
flagLongShort_ <- function(gr, longShort) {
genomeT <- gr |> genome() |> unique()
if(genomeT %in% names(longShort))
gr <- flagLongShort(gr, longShort[[genomeT]])
if("GBreaks" %in% class(gr)) {
genomeQ <- gr$query |> genome() |> unique()
if(genomeQ %in% names(longShort)) {
# sort, flag, unsort, extract flag
grq <- gr$query
grq$idx <- seq_along(grq)
grq <- sort(grq, ignore.strand = TRUE)
grq <- flagLongShort(grq, longShort[[genomeQ]])
gr$query$Arm <- grq$Arm[order(grq$idx)]
}
}
gr
}
longShort <- SimpleList()
longShort$OKI2018.I69 <- loadLongShort("OKI2018_I69.v2/OKI2018_I69.arms.gff3", "OKI2018.I69")
longShort$OSKA2016v1.9 <- loadLongShort("OSKA2016v1.9/OSKA2016v1.9.arms.gff3", "OSKA2016v1.9")
longShort$Bar2.p4 <- loadLongShort("Bar2_p4.Flye/Bar2_p4.Flye.arms.gff3", "Bar2.p4")
longShort## List of length 3
## names(3): OKI2018.I69 OSKA2016v1.9 Bar2.p4Repeat regions
Load from BreakpointsData package via
OikScrambling:::loadAllRepeats()
(reps <- OikScrambling:::loadAllRepeats(compat = FALSE))## List of length 6
## names(6): OKI2018.I69 OSKA2016v1.9 Bar2.p4 KUM.M3.7f AOM.5.5f OdB3
annotateWithReps <- function(x, rep) UseMethod("annotateWithReps")
annotateWithReps.GRanges <- function(x, rep) {
genome <- x |> genome() |> unique()
# Inspired from CAGEr:::ranges2names
o <- findOverlaps(x, rep[[genome]], ignore.strand = TRUE)
o <- as(o, "List")
o <- extractList(rep[[genome]]$Class |> as.character(), o)
o <- endoapply(o, unique)
o[sapply(o, length) == 0] <- NA
x$rep <- o
x
}
overlapLength.GRanges <- function(x, rep) {
genome <- x |> genome() |> unique()
# Inspired from CAGEr:::ranges2names
redRep <- reduce(rep[[genome]])
o <- findOverlaps(x, redRep, ignore.strand = TRUE)
o <- as(o, "List")
repGrl <- extractList(redRep, o)
x$repOvlp <- pintersect(x, repGrl) |> width() |> sum()
x
}
annotateWithReps.GBreaks <- function(x, rep) {
x$query <- annotateWithReps.GRanges(x$query, rep)
x <- annotateWithReps.GRanges(x, rep)
x$query <- overlapLength.GRanges (x$query, rep)
x <- overlapLength.GRanges (x, rep)
x
}
annotateWithReps.SimpleList <- function(x, rep)
sapply(x, annotateWithReps, rep) |> SimpleList()Transcript annotations
(transcripts <- OikScrambling:::loadAllTranscriptsGR(compat = FALSE))## List of length 8
## names(8): OKI2018.I69 OSKA2016v1.9 Bar2.p4 KUM.M3.7f AOM.5.5f OdB3 Ply Ros
annotateWithTranscripts <- function(x, transcripts) UseMethod("annotateWithTranscripts")
annotateWithTranscripts.GRanges <- function(x, transcripts) {
# Taken from CAGEr (and I am the author)
ranges2names <- function (rangesA, rangesB) {
if (is.null(names(rangesB)))
stop(sQuote("rangesB"), " must contain have names.")
names <- findOverlaps(rangesA, rangesB)
names <- as(names, "List")
names <- extractList(names(rangesB), names)
names <- unique(names)
names <- unstrsplit(names, ";")
Rle(names)
}
genomeT <- x |> genome() |> unique()
x$transcripts <- ranges2names(x, transcripts[[genomeT]])
x$transcripts[x$transcripts == ''] <- NA
x
}
annotateWithTranscripts.GBreaks <- function(x, transcripts) {
x$query <- annotateWithTranscripts.GRanges(x$query, transcripts)
x <- annotateWithTranscripts.GRanges(x, transcripts)
x
}
annotateWithTranscripts.SimpleList <- function(x, transcripts)
sapply(x, annotateWithTranscripts, transcripts) |> SimpleList()Mapped alignments
Let’s load data from genome alignments, using the copy distributed in
the BreakpointsData package.
Oikopleura
# Local function to add extra annotation on long/short arms while loading data
load_genomic_breaks_ <- function(file, genomeT, genomeQ, longShort=NULL) {
file <- system.file(paste0("extdata/Oidioi_pairwise_v3/", file), package = "BreakpointsData")
gb <- load_genomic_breaks(file, getBSgenome(genomeT), getBSgenome(genomeQ))
flagLongShort_(gb, longShort)
}
gbs <- SimpleList()
gbs$Oki_Osa <- load_genomic_breaks_("OKI2018_I69_1.0__OSKA2016v1.9.gff.gz", "OKI2018.I69", "OSKA2016v1.9", longShort)
gbs$Oki_Bar <- load_genomic_breaks_("OKI2018_I69_1.0__Bar2_p4.gff.gz", "OKI2018.I69", "Bar2.p4", longShort)
gbs$Oki_Kum <- load_genomic_breaks_("OKI2018_I69_1.0__KUM-M3-7f.gff.gz", "OKI2018.I69", "KUM.M3.7f", longShort)
gbs$Oki_Aom <- load_genomic_breaks_("OKI2018_I69_1.0__AOM-5-5f.gff.gz", "OKI2018.I69", "AOM.5.5f", longShort)
gbs$Oki_Nor <- load_genomic_breaks_("OKI2018_I69_1.0__OdB3.gff.gz", "OKI2018.I69", "OdB3", longShort)
gbs$Osa_Oki <- load_genomic_breaks_("OSKA2016v1.9__OKI2018_I69_1.0.gff.gz", "OSKA2016v1.9", "OKI2018.I69", longShort)
gbs$Osa_Bar <- load_genomic_breaks_("OSKA2016v1.9__Bar2_p4.gff.gz", "OSKA2016v1.9", "Bar2.p4", longShort)
gbs$Osa_Kum <- load_genomic_breaks_("OSKA2016v1.9__KUM-M3-7f.gff.gz", "OSKA2016v1.9", "KUM.M3.7f", longShort)
gbs$Osa_Aom <- load_genomic_breaks_("OSKA2016v1.9__AOM-5-5f.gff.gz", "OSKA2016v1.9", "AOM.5.5f", longShort)
gbs$Osa_Nor <- load_genomic_breaks_("OSKA2016v1.9__OdB3.gff.gz", "OSKA2016v1.9", "OdB3", longShort)
gbs$Bar_Oki <- load_genomic_breaks_("Bar2_p4__OKI2018_I69_1.0.gff.gz", "Bar2.p4", "OKI2018.I69", longShort)
gbs$Bar_Osa <- load_genomic_breaks_("Bar2_p4__OSKA2016v1.9.gff.gz", "Bar2.p4", "OSKA2016v1.9", longShort)
gbs$Bar_Kum <- load_genomic_breaks_("Bar2_p4__KUM-M3-7f.gff.gz", "Bar2.p4", "KUM.M3.7f", longShort)
gbs$Bar_Aom <- load_genomic_breaks_("Bar2_p4__AOM-5-5f.gff.gz", "Bar2.p4", "AOM.5.5f", longShort)
gbs$Bar_Nor <- load_genomic_breaks_("Bar2_p4__OdB3.gff.gz", "Bar2.p4", "OdB3", longShort)
Oik_Oik <- names(gbs)Ciona
gbs$Ply_Ros <- load_genomic_breaks(system.file("extdata/Ciona_pairwise_v3/C_int_P__C_int_R.gff.gz", package = "BreakpointsData"), NULL, NULL)
gbs$Ply_Rob <- load_genomic_breaks(system.file("extdata/Ciona_pairwise_v3/C_int_P__C_rob_HT.gff.gz", package = "BreakpointsData"), NULL, NULL)
gbs$Ply_Sav <- load_genomic_breaks(system.file("extdata/Ciona_pairwise_v3/C_int_P__C_sav.gff.gz", package = "BreakpointsData"), NULL, NULL)
gbs$Ply_Oki <- load_genomic_breaks(system.file("extdata/Ciona_pairwise_v3/C_int_P__OKI2018_I69_1.0.gff.gz", package = "BreakpointsData"), NULL, genomes$OKI2018.I69)
gbs$Rob_Ros <- load_genomic_breaks(system.file("extdata/Ciona_pairwise_v3/C_rob_HT__C_int_R.gff.gz", package = "BreakpointsData"), NULL, NULL)
gbs$Rob_Ply <- load_genomic_breaks(system.file("extdata/Ciona_pairwise_v3/C_rob_HT__C_int_P.gff.gz", package = "BreakpointsData"), NULL, NULL)
gbs$Rob_Sav <- load_genomic_breaks(system.file("extdata/Ciona_pairwise_v3/C_rob_HT__C_sav.gff.gz", package = "BreakpointsData"), NULL, NULL)
gbs$Rob_Oki <- load_genomic_breaks(system.file("extdata/Ciona_pairwise_v3/C_rob_HT__OKI2018_I69_1.0.gff.gz", package = "BreakpointsData"), NULL, genomes$OKI2018.I69)Drosophila
gbs$Dme_Dbu <- load_genomic_breaks(system.file("extdata/Insects_pairwise_v3/Dmel__Dbus_ASM1175060v1.gff.gz", package = "BreakpointsData"), NULL, NULL)
gbs$Dme_Dsu <- load_genomic_breaks(system.file("extdata/Insects_pairwise_v3/Dmel__RU_Dsub_v1.1.gff.gz", package = "BreakpointsData"), NULL, NULL)
gbs$Dme_Dya <- load_genomic_breaks(system.file("extdata/Insects_pairwise_v3/Dmel__Prin_Dyak_Tai18E2_2.0.gff.gz", package = "BreakpointsData"), NULL, NULL)
gbs$Dme_Dma <- load_genomic_breaks(system.file("extdata/Insects_pairwise_v3/Dmel__Dmau_ASM438214v1.gff.gz", package = "BreakpointsData"), NULL, NULL)Caenorhabditis
gbs$Cni_Cbr <- load_genomic_breaks(system.file("extdata/Nematodes_pairwise/nigoni_briggsae.07.postmasked.gff.gz", package = "BreakpointsData"), type = "match")
gbs$Cni_Cre <- load_genomic_breaks(system.file("extdata/Nematodes_pairwise/nigoni_remanei.07.postmasked.gff.gz", package = "BreakpointsData"), type = "match")
gbs$Cni_Cin <- load_genomic_breaks(system.file("extdata/Nematodes_pairwise/nigoni_inopinata.07.postmasked.gff.gz", package = "BreakpointsData"), type = "match")
gbs$Cbr_Cni <- load_genomic_breaks(system.file("extdata/Nematodes_pairwise/briggsae_nigoni.07.postmasked.gff.gz", package = "BreakpointsData"), type = "match")
gbs$Cbr_Cre <- load_genomic_breaks(system.file("extdata/Nematodes_pairwise/briggsae_remanei.07.postmasked.gff.gz", package = "BreakpointsData"), type = "match")
gbs$Cbr_Cel <- load_genomic_breaks(system.file("extdata/Nematodes_pairwise/briggsae_elegans.07.postmasked.gff.gz", package = "BreakpointsData"), type = "match")Annotate Oikopleura
gbs[Oik_Oik] <- annotateWithReps(gbs[Oik_Oik], reps)
gbs[Oik_Oik] <- annotateWithTranscripts(gbs[Oik_Oik], transcripts)
gbs <- sapply(gbs, flagAll) |> SimpleList()Unaligned regions
Note that the unaligned regions are strandless and unpaired by definition.
unal <- BiocParallel::bplapply(gbs, cleanGaps) |> SimpleList()
unal[Oik_Oik] <- BiocParallel::bplapply(unal[Oik_Oik], flagLongShort_, longShort)
unal[Oik_Oik] <- BiocParallel::bplapply(unal[Oik_Oik], annotateWithReps, reps)
unal[Oik_Oik] <- BiocParallel::bplapply(unal[Oik_Oik], annotateWithTranscripts, transcripts)Coalescing alignments
Coalesce
We call these coalesced regions “mapped regions”. Some of the bases in the region are aligned and some not (see the “mapped unaligned regions” later).
coa <- BiocParallel::bplapply(gbs, coalesce_contigs) |> SimpleList()
coa[Oik_Oik] <- BiocParallel::bplapply(coa[Oik_Oik], flagLongShort_, longShort)
coa[Oik_Oik] <- annotateWithReps(coa[Oik_Oik], reps)
coa[Oik_Oik] <- annotateWithTranscripts(coa[Oik_Oik], transcripts)
coa <- sapply(coa, flagAll) |> SimpleList()Unmapped regions
Generate
We can not call them “uncoalesced” because this would also qualify aligned regions that were not colinear with any other region.
unmap <- BiocParallel::bplapply(coa, cleanGaps) |> SimpleList()
unmap[Oik_Oik] <- BiocParallel::bplapply(unmap[Oik_Oik], flagLongShort_, longShort)
unmap[Oik_Oik] <- BiocParallel::bplapply(unmap[Oik_Oik], annotateWithReps, reps)
unmap[Oik_Oik] <- BiocParallel::bplapply(unmap[Oik_Oik], annotateWithTranscripts, transcripts)Whole-genome objects
Let’s have objects that cover the whole genomes (with the possible
exception of the telomeric regions) and contain isolated
alignments, breakpoint regions, colinear
alignments and bridge regions. These are
GRanges objects, not GBreaks, since they
contain unaligned regions.
makeWholeGenomeObject <- function(aligned, unaligned) {
# Isolated alignments are aligned regions not in collinear regions
iso <- granges(aligned[aligned$nonCoa]) |> plyranges::mutate(type = "isolated alignment")
# Breakpoint regions are unaligned regions not in collinear regions
brk <- granges(unaligned[unaligned$nonCoa])|> plyranges::mutate(type = "breakpoint region")
# Collinear alignments are aligned regions in collinear regions
col <- granges(aligned[!aligned$nonCoa]) |> plyranges::mutate(type = "collinear alignment")
# Bridge regions are unaligned regions in collinear regions
bri <- granges(unaligned[!unaligned$nonCoa]) |> plyranges::mutate(type = "bridge region")
wholeGenome <- c(iso, brk, col, bri) |> sort(ignore.strand = TRUE)
wholeGenome$type <- factor(wholeGenome$type)
wholeGenome
}
wgo <- mapply(makeWholeGenomeObject, gbs, unal) |> SimpleList()
for_wgo_barplots <- sapply(wgo, \(gr) tapply(width(gr), gr$type, sum)) |>
as.data.frame() |>
tibble::as_tibble(rownames = "type") |>
tidyr::pivot_longer(!type) |>
dplyr::mutate(distClass = OikScrambling:::compDistClass(name)) |>
dplyr::mutate(genus = OikScrambling:::compGenus(name))
p1 <- ggplot(for_wgo_barplots |> dplyr::filter(genus == "Oikopleura", distClass == "distant")) +
aes(name, value, fill = type) +
ggplot2::coord_flip() +
geom_bar( stat = "identity") +
ggtitle("Oki or Kume vs other populations")
p2 <- ggplot(for_wgo_barplots |> dplyr::filter(genus == "Oikopleura", distClass == "intermediate")) +
aes(name, value, fill = type) +
ggplot2::coord_flip() +
geom_bar( stat = "identity") +
ggtitle("North Atlantic vs North Pacific")
p3 <- ggplot(for_wgo_barplots |> dplyr::filter(genus == "Oikopleura", distClass == "same_or_sister")) +
aes(name, value, fill = type) +
ggplot2::coord_flip() +
geom_bar( stat = "identity") +
ggtitle("same population")
p4 <- ggplot(for_wgo_barplots |> dplyr::filter(genus == "Drosophila")) +
aes(name, value, fill = type) +
ggplot2::coord_flip() +
geom_bar( stat = "identity") +
ggtitle("Drosophila (various evol. distances)")
p5 <- ggplot(for_wgo_barplots |> dplyr::filter(genus == "Ciona")) +
aes(name, value, fill = type) +
ggplot2::coord_flip() +
geom_bar( stat = "identity") +
ggtitle("Ciona (various evol. distances)")
p6 <- ggplot(for_wgo_barplots |> dplyr::filter(genus == "Caenorhabditis")) +
aes(name, value, fill = type) +
ggplot2::coord_flip() +
geom_bar( stat = "identity") +
ggtitle("Caenorhabditis (various evol. distances)")We can see that:
- The larger size of Okinawa and Kume genomes is explained by sequences that are not aligned. (Repeats ?)
- The fraction of isolated alignments is always small, but it is comparatively larger in Oiks compared to Drosophila and Ciona.
- The fraction of bridge regions increases with evolutionary distance, until becoming larger than the fraction of colinear alignments (D. melanogaster / D. buskii, C. savignyi / C intestinalis or robusta).
library("patchwork")
p1 / p2 / p3 / p4 / p5 / p6
In the next plot, replicate pairs of genomes are merged.
for_wgo_barplots2 <- sapply(wgo, \(gr) tapply(width(gr), gr$type, sum)) |>
prop.table(2) |>
as.data.frame()
for_wgo_barplots2$Osa_Oki <- rowMeans(for_wgo_barplots2[,c("Osa_Oki", "Oki_Osa")])
for_wgo_barplots2$Oki_Osa <- NULL
for_wgo_barplots2$Bar_Oki <- rowMeans(for_wgo_barplots2[,c("Bar_Oki", "Oki_Bar")])
for_wgo_barplots2$Oki_Bar <- NULL
for_wgo_barplots2$Osa_Bar <- rowMeans(for_wgo_barplots2[,c("Osa_Bar", "Bar_Osa")])
for_wgo_barplots2$Bar_Osa <- NULL
for_wgo_barplots2 <- for_wgo_barplots2 |>
tibble::as_tibble(rownames = "type") |>
tidyr::pivot_longer(!type) |>
dplyr::mutate(distClass = OikScrambling:::compDistClass(name)) |>
dplyr::mutate(genus = OikScrambling:::compGenus(name))
for_wgo_barplots2$type <- for_wgo_barplots2$type |> factor(c("isolated alignment", "bridge region", "collinear alignment", "breakpoint region"))
for_wgo_barplots2## # A tibble: 120 × 5
## type name value distClass genus
## <fct> <chr> <dbl> <fct> <fct>
## 1 breakpoint region Oki_Kum 0.0723 same_or_sister Oikopleura
## 2 breakpoint region Oki_Aom 0.279 distant Oikopleura
## 3 breakpoint region Oki_Nor 0.315 distant Oikopleura
## 4 breakpoint region Osa_Oki 0.254 distant Oikopleura
## 5 breakpoint region Osa_Bar 0.157 intermediate Oikopleura
## 6 breakpoint region Osa_Kum 0.227 distant Oikopleura
## 7 breakpoint region Osa_Aom 0.0705 same_or_sister Oikopleura
## 8 breakpoint region Osa_Nor 0.162 intermediate Oikopleura
## 9 breakpoint region Bar_Oki 0.269 distant Oikopleura
## 10 breakpoint region Bar_Kum 0.254 distant Oikopleura
## # ℹ 110 more rows
for_wgo_barplots2$distClass <-
factor(for_wgo_barplots2$distClass,
labels=c("Same species", "Close", "Intermediate", "Distant", "Different_genus"))
for_wgo_barplots2$name <- for_wgo_barplots2$name |> toupper() |> sub(pat="_", rep="–")
for_wgo_barplots2$type <-
factor(for_wgo_barplots2$type,
labels = c("Isolated alignment", "Bridge region", "Collinear alignment", "Breakpoint region"))
ggplot(for_wgo_barplots2 |> dplyr::filter(genus == "Oikopleura")) +
aes(name, value, fill = type) +
ggplot2::coord_flip() +
geom_bar( stat = "identity", color = "black", linewidth = 0.2) +
ggtitle("Proportion of the genome in aligned, bridge and breakpoint regions") +
facet_grid(distClass ~ ., scales = "free", space = "free") +
theme_bw() +
scale_y_continuous("", labels = scales::percent_format(accuracy = 5L), position = "right") +
scale_x_discrete("") +
scale_fill_manual(values = c("#f79e87", "#8dd3c7", "#80b1d3", "#f9f5b0"))## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–BAR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–NOR' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OSA–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–KUM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'BAR–OKI' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <e2>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <80>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## conversion failure on 'OKI–AOM' in 'mbcsToSbcs': dot substituted for <93>## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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Translocated regions
Here we compute new GBreaks objects representing the
intervals between two regions that would be colinear if there would not
be a translocation separating them.
traGaps <- function(coa) {
# The input MUST already be coalesced.
tra <- flagTranslocations(coa)
# Consider both sides
tra$tra <- tra$tra | tra$query$tra
# Then, remove translocated regions
tra <- filterTranslocations(tra, remove = TRUE)
# Finally, extract the newly "unaligned mapped" regions.
# They contain the gaps left by the removal of the translocated regions.
bridgeRegions(tra)
}
tra <- BiocParallel::bplapply(coa, traGaps) |> as("SimpleList")
tra[Oik_Oik] <- BiocParallel::bplapply(tra[Oik_Oik], flagLongShort_, longShort)
tra[Oik_Oik] <- annotateWithReps(tra[Oik_Oik], reps)
tra[Oik_Oik] <- annotateWithTranscripts(tra[Oik_Oik], transcripts)Coalesce again
We remove the translocated regions that interrupt colinearity, where one of the colinear pairs is closer than 200 bp.
removeTranslocationsOnTargetGenome <- function(gb) {
gb <- flagTranslocations(gb)
gb <- dist2next(gb, step = 2, ignore.strand = TRUE)
idx <- 1 + which( gb$tra & (gb$tdist < 200 | gb$qdist < 200) )
if(length(idx) != 0)
gb <- gb[-idx]
coalesce_contigs(gb)
}
removeTranslocationsOnBothGenomes <- function(gb)
gb |>
removeTranslocationsOnTargetGenome() |>
swap() |> sort(i=T) |>
removeTranslocationsOnTargetGenome() |>
swap() |> sort(i=T)
coa2 <- BiocParallel::bplapply(coa, removeTranslocationsOnBothGenomes) |> SimpleList()
coa2[Oik_Oik] <- BiocParallel::bplapply(coa2[Oik_Oik], flagLongShort_, longShort)
coa2[Oik_Oik] <- annotateWithReps(coa2[Oik_Oik], reps)
coa2[Oik_Oik] <- annotateWithTranscripts(coa2[Oik_Oik], transcripts)
coa2 <- sapply(coa2, flagAll) |> SimpleList()Unmapped regions 2
The intervals between double-coalesced regions.
unmap2 <- BiocParallel::bplapply(coa2, cleanGaps) |> SimpleList()
unmap2[Oik_Oik] <- BiocParallel::bplapply(unmap2[Oik_Oik], flagLongShort_, longShort)
unmap2[Oik_Oik] <- BiocParallel::bplapply(unmap2[Oik_Oik], annotateWithReps, reps)
unmap2[Oik_Oik] <- BiocParallel::bplapply(unmap2[Oik_Oik], annotateWithTranscripts, transcripts)Numbers of blocks
bp_summary <-
rbind(
gbs = sapply(gbs, length),
unal = sapply(unal, length),
coa = sapply(coa, length),
unmap = sapply(unmap, length),
unmap2 = sapply(unmap2, length),
bri = sapply(bri, length),
tra = sapply(tra, length),
tra2 = sapply(tra2, length),
coa2 = sapply(coa2, length)
) |> t() |> data.frame()
sapply(bp_summary, \(x) tapply(x, row.names(bp_summary) |> OikScrambling:::compDistance(), mean))## gbs unal coa unmap unmap2 bri tra
## Cbr_Cel 47012.00 46608.00 3686.000 3675.000 3536.000 43326.000 363.0000
## Cbr_Cni 51726.00 49877.00 10015.000 9394.000 6358.000 41711.000 1839.0000
## Cbr_Cre 44819.00 44593.00 3446.000 3434.000 3266.000 41373.000 371.0000
## Cni_Cbr 51324.00 49573.00 9837.000 9504.000 6349.000 41487.000 1339.0000
## Cni_Cin 41207.00 40942.00 2860.000 2853.000 2805.000 38347.000 302.0000
## Cni_Cre 44877.00 44650.00 3488.000 3480.000 3286.000 41389.000 339.0000
## Dme_Dbu 47893.00 47867.00 5959.000 5951.000 5869.000 41934.000 356.0000
## Dme_Dma 9732.00 9138.00 2706.000 2616.000 2215.000 7026.000 216.0000
## Dme_Dsu 68750.00 68626.00 992.000 984.000 870.000 67758.000 116.0000
## Dme_Dya 23059.00 22743.00 1816.000 1776.000 1553.000 21243.000 142.0000
## In same pop 15177.00 12652.67 5520.667 4465.333 2446.333 9656.333 1124.3333
## Int – Int 40659.00 36133.00 7701.000 6304.000 3727.000 32958.000 1070.0000
## Int – Rob 58863.00 56141.33 4782.333 4432.667 2975.333 54080.667 594.3333
## Int/Rob – Oki 2237.00 2221.50 1354.000 1339.500 1337.500 883.000 6.5000
## Int/Rob – Sav 69332.00 69275.00 4094.500 4068.500 4063.500 65237.500 223.0000
## North – North 24623.75 24125.25 4394.500 4333.000 3630.250 20229.250 415.2500
## Oki – North 31309.00 31115.50 8718.625 8700.875 8033.875 22590.375 465.6250
## tra2 coa2
## Cbr_Cel 332.0000 3546.000
## Cbr_Cni 1096.0000 6677.000
## Cbr_Cre 331.0000 3274.000
## Cni_Cbr 712.0000 6479.000
## Cni_Cin 295.0000 2811.000
## Cni_Cre 298.0000 3292.000
## Dme_Dbu 323.0000 5877.000
## Dme_Dma 114.0000 2272.000
## Dme_Dsu 94.0000 878.000
## Dme_Dya 80.0000 1582.000
## In same pop 328.6667 2733.333
## Int – Int 378.0000 4224.000
## Int – Rob 309.0000 3172.333
## Int/Rob – Oki 6.5000 1352.000
## Int/Rob – Sav 221.5000 4089.500
## North – North 205.5000 3670.750
## Oki – North 268.1250 8046.500
sapply(bp_summary, \(x) tapply(x, row.names(bp_summary) |> OikScrambling:::compDistance(), median))## gbs unal coa unmap unmap2 bri tra tra2 coa2
## Cbr_Cel 47012 46608.0 3686.0 3675.0 3536.0 43326.0 363.0 332.0 3546.0
## Cbr_Cni 51726 49877.0 10015.0 9394.0 6358.0 41711.0 1839.0 1096.0 6677.0
## Cbr_Cre 44819 44593.0 3446.0 3434.0 3266.0 41373.0 371.0 331.0 3274.0
## Cni_Cbr 51324 49573.0 9837.0 9504.0 6349.0 41487.0 1339.0 712.0 6479.0
## Cni_Cin 41207 40942.0 2860.0 2853.0 2805.0 38347.0 302.0 295.0 2811.0
## Cni_Cre 44877 44650.0 3488.0 3480.0 3286.0 41389.0 339.0 298.0 3292.0
## Dme_Dbu 47893 47867.0 5959.0 5951.0 5869.0 41934.0 356.0 323.0 5877.0
## Dme_Dma 9732 9138.0 2706.0 2616.0 2215.0 7026.0 216.0 114.0 2272.0
## Dme_Dsu 68750 68626.0 992.0 984.0 870.0 67758.0 116.0 94.0 878.0
## Dme_Dya 23059 22743.0 1816.0 1776.0 1553.0 21243.0 142.0 80.0 1582.0
## In same pop 15184 12425.0 5424.0 4119.0 2042.0 9662.0 1149.0 261.0 2256.0
## Int – Int 40659 36133.0 7701.0 6304.0 3727.0 32958.0 1070.0 378.0 4224.0
## Int – Rob 60205 57513.0 4812.0 4431.0 3006.0 55393.0 592.0 322.0 3152.0
## Int/Rob – Oki 2237 2221.5 1354.0 1339.5 1337.5 883.0 6.5 6.5 1352.0
## Int/Rob – Sav 69332 69275.0 4094.5 4068.5 4063.5 65237.5 223.0 221.5 4089.5
## North – North 24607 24103.5 4139.0 4081.5 3369.0 20434.5 403.0 182.5 3412.5
## Oki – North 31252 31041.5 8806.0 8785.0 8090.5 22446.0 453.0 258.5 8105.0
sapply(bp_summary, \(x) tapply(x, row.names(bp_summary) |> OikScrambling:::compDistance(), sd))## gbs unal coa unmap unmap2 bri
## Cbr_Cel NA NA NA NA NA NA
## Cbr_Cni NA NA NA NA NA NA
## Cbr_Cre NA NA NA NA NA NA
## Cni_Cbr NA NA NA NA NA NA
## Cni_Cin NA NA NA NA NA NA
## Cni_Cre NA NA NA NA NA NA
## Dme_Dbu NA NA NA NA NA NA
## Dme_Dma NA NA NA NA NA NA
## Dme_Dsu NA NA NA NA NA NA
## Dme_Dya NA NA NA NA NA NA
## In same pop 87.70975 428.5491 624.63536 648.96867 1252.44574 657.51831
## Int – Int NA NA NA NA NA NA
## Int – Rob 2481.04555 2535.0468 203.13132 234.50444 97.67975 2649.62381
## Int/Rob – Oki 155.56349 154.8564 67.88225 67.17514 67.17514 87.68124
## Int/Rob – Sav 1228.95159 1210.5668 75.66043 58.68986 58.68986 1153.29116
## North – North 194.88693 114.1034 557.88499 554.44447 549.00357 663.36585
## Oki – North 772.56974 758.8316 168.79653 165.44782 164.13795 839.21391
## tra tra2 coa2
## Cbr_Cel NA NA NA
## Cbr_Cni NA NA NA
## Cbr_Cre NA NA NA
## Cni_Cbr NA NA NA
## Cni_Cin NA NA NA
## Cni_Cre NA NA NA
## Dme_Dbu NA NA NA
## Dme_Dma NA NA NA
## Dme_Dsu NA NA NA
## Dme_Dya NA NA NA
## In same pop 172.329142 150.3872778 1409.00473
## Int – Int NA NA NA
## Int – Rob 27.574142 28.7923601 107.94597
## Int/Rob – Oki 4.949747 4.9497475 67.88225
## Int/Rob – Sav 1.414214 0.7071068 75.66043
## North – North 54.628289 74.8264659 554.36894
## Oki – North 37.709178 32.1178077 166.26055Fraction of the genome aligned or mapped
aligned_tot <- sapply(gbs, \(x) sum(width(x)))
mapped_tot <- sapply(coa, \(x) sum(width(x)))
mapped2_tot <- sapply(coa2, \(x) sum(width(x)))
unaligned_tot <- sapply(unal, \(x) sum(width(x)))
unmapped_tot <- sapply(unmap, \(x) sum(width(x)))
unmapped2_tot <- sapply(unmap2, \(x) sum(width(x)))
(align_summary <- 100 * cbind(
align_frac = aligned_tot / ( aligned_tot + unaligned_tot ),
map_frac = mapped_tot / ( mapped_tot + unmapped_tot ),
map2_frac = mapped2_tot / ( mapped2_tot + unmapped2_tot)
)|> as.data.frame())## align_frac map_frac map2_frac
## Oki_Osa 52.0159495 72.064774 72.591841
## Oki_Bar 50.2331439 71.873745 72.439411
## Oki_Kum 83.7160367 92.765000 94.480041
## Oki_Aom 50.6089555 72.114976 72.741460
## Oki_Nor 47.1467623 68.537624 69.073404
## Osa_Oki 58.3631347 77.105711 77.170651
## Osa_Bar 71.1871466 85.560773 86.174793
## Osa_Kum 58.4606442 77.300551 77.474092
## Osa_Aom 86.4673469 92.945330 94.144071
## Osa_Nor 68.8797738 83.812429 84.344633
## Bar_Oki 55.7960607 74.409334 74.396050
## Bar_Osa 70.9620899 82.982915 83.029837
## Bar_Kum 56.6319075 74.633503 74.605171
## Bar_Aom 71.3391619 83.174402 83.438869
## Bar_Nor 82.0574520 88.611295 89.137858
## Ply_Ros 81.3622209 91.050237 92.176488
## Ply_Rob 70.3529758 87.498052 88.962676
## Ply_Sav 13.1367749 67.169476 67.181135
## Ply_Oki 0.6063520 1.897941 1.897793
## Rob_Ros 73.6319134 90.562151 91.221000
## Rob_Ply 73.0152650 89.704745 90.321434
## Rob_Sav 14.5141690 70.474445 70.494999
## Rob_Oki 0.6696567 2.112460 2.112311
## Dme_Dbu 21.7446598 71.124298 71.647394
## Dme_Dsu 59.8730476 76.684629 76.712764
## Dme_Dya 76.9451636 84.778190 84.900306
## Dme_Dma 80.9637966 85.833201 86.001342
## Cni_Cbr 58.1113573 78.883789 81.461788
## Cni_Cre 25.6219631 68.943364 69.262266
## Cni_Cin 16.4215656 61.757050 61.773933
## Cbr_Cni 70.0267232 91.250713 92.327842
## Cbr_Cre 31.0274058 76.963157 77.275637
## Cbr_Cel 23.5125532 70.379746 70.589716
sapply(align_summary, \(x) tapply(x, row.names(align_summary) |> OikScrambling:::compDistance(), mean)) |> round(1)## align_frac map_frac map2_frac
## Cbr_Cel 23.5 70.4 70.6
## Cbr_Cni 70.0 91.3 92.3
## Cbr_Cre 31.0 77.0 77.3
## Cni_Cbr 58.1 78.9 81.5
## Cni_Cin 16.4 61.8 61.8
## Cni_Cre 25.6 68.9 69.3
## Dme_Dbu 21.7 71.1 71.6
## Dme_Dma 81.0 85.8 86.0
## Dme_Dsu 59.9 76.7 76.7
## Dme_Dya 76.9 84.8 84.9
## In same pop 84.1 91.4 92.6
## Int – Int 81.4 91.1 92.2
## Int – Rob 72.3 89.3 90.2
## Int/Rob – Oki 0.6 2.0 2.0
## Int/Rob – Sav 13.8 68.8 68.8
## North – North 70.6 83.9 84.2
## Oki – North 53.7 73.5 73.8
sapply(align_summary, \(x) tapply(x, row.names(align_summary) |> OikScrambling:::compDistance(), median)) |> round(1)## align_frac map_frac map2_frac
## Cbr_Cel 23.5 70.4 70.6
## Cbr_Cni 70.0 91.3 92.3
## Cbr_Cre 31.0 77.0 77.3
## Cni_Cbr 58.1 78.9 81.5
## Cni_Cin 16.4 61.8 61.8
## Cni_Cre 25.6 68.9 69.3
## Dme_Dbu 21.7 71.1 71.6
## Dme_Dma 81.0 85.8 86.0
## Dme_Dsu 59.9 76.7 76.7
## Dme_Dya 76.9 84.8 84.9
## In same pop 83.7 92.8 94.1
## Int – Int 81.4 91.1 92.2
## Int – Rob 73.0 89.7 90.3
## Int/Rob – Oki 0.6 2.0 2.0
## Int/Rob – Sav 13.8 68.8 68.8
## North – North 71.1 83.5 83.9
## Oki – North 53.9 73.3 73.6
sapply(align_summary, \(x) tapply(x, row.names(align_summary) |> OikScrambling:::compDistance(), sd)) |> round(1)## align_frac map_frac map2_frac
## Cbr_Cel NA NA NA
## Cbr_Cni NA NA NA
## Cbr_Cre NA NA NA
## Cni_Cbr NA NA NA
## Cni_Cin NA NA NA
## Cni_Cre NA NA NA
## Dme_Dbu NA NA NA
## Dme_Dma NA NA NA
## Dme_Dsu NA NA NA
## Dme_Dya NA NA NA
## In same pop 2.2 2.5 3.0
## Int – Int NA NA NA
## Int – Rob 1.7 1.6 1.1
## Int/Rob – Oki 0.0 0.2 0.2
## Int/Rob – Sav 1.0 2.3 2.3
## North – North 1.2 1.2 1.4
## Oki – North 4.2 2.9 2.7Summary
df <- cbind(
gbs = sapply(gbs, length),
coa = sapply(coa, length),
coa2 = sapply(coa2, length)
) |> as.data.frame() |>
dplyr::arrange(gbs = gbs - coa - coa2, coa = coa - coa2)
df$pair <- row.names(df)
ggplot(df |> tidyr::pivot_longer(!pair)) +
aes(pair, value, fill = name) +
geom_bar( stat = "identity" ) +
ggplot2::coord_flip() +
ggtitle("Cumulative plot (gbs ⊃ coa ⊃ coa2) of the computed genomic regions")
Save data
save(gbs, unal, coa, unmap, bri, tra, tra2, coa2, unmap2, wgo, longShort, file = "BreakPoints.Rdata")
system("echo '02c664188e12f1264a96b717e16e1d5e BreakPoints.Rdata' | md5sum -c", intern = TRUE)## Warning in system("echo '02c664188e12f1264a96b717e16e1d5e BreakPoints.Rdata' |
## md5sum -c", : running command 'echo '02c664188e12f1264a96b717e16e1d5e
## BreakPoints.Rdata' | md5sum -c' had status 1## [1] "BreakPoints.Rdata: FAILED"
## attr(,"status")
## [1] 1Session information
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 12 (bookworm)
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
##
## locale:
## [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
## [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
## [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] patchwork_1.1.2
## [2] BSgenome.Oidioi.genoscope.OdB3_1.0.0
## [3] BSgenome.Oidioi.OIST.AOM.5.5f_1.0.1
## [4] BSgenome.Oidioi.OIST.KUM.M3.7f_1.0.1
## [5] BSgenome.Oidioi.OIST.Bar2.p4_1.0.1
## [6] BSgenome.Oidioi.OIST.OSKA2016v1.9_1.0.0
## [7] BSgenome.Oidioi.OIST.OKI2018.I69_1.0.1
## [8] BSgenome_1.68.0
## [9] rtracklayer_1.60.0
## [10] Biostrings_2.68.1
## [11] XVector_0.40.0
## [12] BreakpointsData_3.10.1
## [13] ggplot2_3.4.3
## [14] GenomicBreaks_0.14.2
## [15] GenomicRanges_1.52.0
## [16] GenomeInfoDb_1.36.1
## [17] IRanges_2.34.1
## [18] S4Vectors_0.38.1
## [19] BiocGenerics_0.46.0
##
## loaded via a namespace (and not attached):
## [1] splines_4.3.1 BiocIO_1.10.0
## [3] filelock_1.0.2 bitops_1.0-7
## [5] tibble_3.2.1 R.oo_1.25.0
## [7] XML_3.99-0.14 rpart_4.1.19
## [9] lifecycle_1.0.3 rprojroot_2.0.3
## [11] lattice_0.20-45 MASS_7.3-58.2
## [13] backports_1.4.1 magrittr_2.0.3
## [15] Hmisc_5.1-0 sass_0.4.7
## [17] rmarkdown_2.23 jquerylib_0.1.4
## [19] yaml_2.3.7 plotrix_3.8-2
## [21] DBI_1.1.3 OikScrambling_5.0.0
## [23] CNEr_1.36.0 minqa_1.2.5
## [25] RColorBrewer_1.1-3 ade4_1.7-22
## [27] abind_1.4-5 zlibbioc_1.46.0
## [29] purrr_1.0.2 R.utils_2.12.2
## [31] RCurl_1.98-1.12 nnet_7.3-18
## [33] pracma_2.4.2 rappdirs_0.3.3
## [35] GenomeInfoDbData_1.2.10 gdata_2.19.0
## [37] annotate_1.78.0 pkgdown_2.0.7
## [39] codetools_0.2-19 DelayedArray_0.26.7
## [41] xml2_1.3.5 tidyselect_1.2.0
## [43] shape_1.4.6 farver_2.1.1
## [45] lme4_1.1-34 BiocFileCache_2.8.0
## [47] matrixStats_1.0.0 base64enc_0.1-3
## [49] GenomicAlignments_1.36.0 jsonlite_1.8.7
## [51] mitml_0.4-5 Formula_1.2-5
## [53] survival_3.5-3 iterators_1.0.14
## [55] systemfonts_1.0.5 foreach_1.5.2
## [57] progress_1.2.2 tools_4.3.1
## [59] ragg_1.2.5 Rcpp_1.0.11
## [61] glue_1.6.2 gridExtra_2.3
## [63] pan_1.8 xfun_0.40
## [65] MatrixGenerics_1.12.2 EBImage_4.42.0
## [67] dplyr_1.1.3 withr_2.5.1
## [69] fastmap_1.1.1 boot_1.3-28.1
## [71] fansi_1.0.5 digest_0.6.33
## [73] R6_2.5.1 mice_3.16.0
## [75] textshaping_0.3.7 colorspace_2.1-0
## [77] GO.db_3.17.0 gtools_3.9.4
## [79] poweRlaw_0.70.6 biomaRt_2.56.1
## [81] jpeg_0.1-10 RSQLite_2.3.1
## [83] weights_1.0.4 R.methodsS3_1.8.2
## [85] utf8_1.2.3 tidyr_1.3.0
## [87] generics_0.1.3 data.table_1.14.8
## [89] prettyunits_1.2.0 httr_1.4.7
## [91] htmlwidgets_1.6.2 S4Arrays_1.0.5
## [93] pkgconfig_2.0.3 gtable_0.3.4
## [95] blob_1.2.4 htmltools_0.5.6.1
## [97] fftwtools_0.9-11 plyranges_1.20.0
## [99] scales_1.2.1 Biobase_2.60.0
## [101] png_0.1-8 knitr_1.44
## [103] heatmaps_1.24.0 rstudioapi_0.15.0
## [105] tzdb_0.4.0 reshape2_1.4.4
## [107] rjson_0.2.21 curl_5.1.0
## [109] checkmate_2.2.0 nlme_3.1-162
## [111] nloptr_2.0.3 cachem_1.0.8
## [113] stringr_1.5.0 KernSmooth_2.23-20
## [115] parallel_4.3.1 genoPlotR_0.8.11
## [117] foreign_0.8-84 AnnotationDbi_1.62.2
## [119] restfulr_0.0.15 desc_1.4.2
## [121] pillar_1.9.0 grid_4.3.1
## [123] vctrs_0.6.3 jomo_2.7-6
## [125] dbplyr_2.3.3 xtable_1.8-4
## [127] cluster_2.1.4 htmlTable_2.4.1
## [129] evaluate_0.22 GenomicFeatures_1.52.1
## [131] readr_2.1.4 cli_3.6.1
## [133] locfit_1.5-9.8 compiler_4.3.1
## [135] Rsamtools_2.16.0 rlang_1.1.1
## [137] crayon_1.5.2 labeling_0.4.3
## [139] plyr_1.8.8 fs_1.6.3
## [141] stringi_1.7.12 BiocParallel_1.34.2
## [143] munsell_0.5.0 tiff_0.1-11
## [145] glmnet_4.1-7 Matrix_1.5-3
## [147] hms_1.1.3 bit64_4.0.5
## [149] KEGGREST_1.40.0 SummarizedExperiment_1.30.2
## [151] broom_1.0.5 memoise_2.0.1
## [153] bslib_0.5.1 bit_4.0.5