Let's make a Christmas tree!

library(topcorneR) |> suppressPackageStartupMessages()

Let’s paint a Christmas tree in a 96-well plate by transferring colored inks!

Result

We ran this transfer in February 2018 during a demo at RIKEN.

image

Let’s see how it was prepared!

Planning the result

First, let’s create a Plate object that represents the expected result of the transfer.

planPlate <- Plate("384")

Our tree has a stem, …

planPlate <- set_block(planPlate, "H21~I24", "stem", 1000)

… and green leaves …

planPlate <- planPlate |>
  set_block("B19~O20", "leaves", 1000) |>
  set_block("C17~N18", "leaves", 1000) |>
  set_block("D15~M16", "leaves", 1000) |>
  set_block("E13~L14", "leaves", 1000) |>
  set_block("F09~K12", "leaves", 1000) |>
  set_block("G05~J08", "leaves", 1000) |>
  set_block("H02~I04", "leaves", 1000)

… and is decorated with balls.

planPlate <- planPlate |>
  set_block("G05", "balls", 1000) |>
  set_block("J08", "balls", 1000) |>
  set_block("F13", "balls", 1000) |>
  set_block("J12", "balls", 1000) |>
  set_block("I17", "balls", 1000) |>
  set_block("E18", "balls", 1000) |>
  set_block("M16", "balls", 1000)

# Remove leaves where balls are
planPlate[!is.na(planPlate$balls),"leaves"] <- NA

Let’s visualise the Plate object

plateMap <- function(plate, x, title) {
  platetools::raw_map(plate[[x]], well=rownames(plate), plate="384") +
  ggplot2::ggtitle(title)
}
(plot_stem   <- plateMap(planPlate, "stem",   "stem"))

(plot_leaves <- plateMap(planPlate, "leaves", "leaves"))

(plot_balls  <- plateMap(planPlate, "balls",  "balls"))

plateMap_all <- function(plate) {
  x <- lapply(colnames(plate), function(x) ifelse(is.na(plate[,x]), "", x))
  names(x) <- colnames(plate)
  x <- as.data.frame(x)
  x <- apply( x, 1
            , function(x)
                if(all(x=="")) {
                  NA
                } else {
                  paste(unique(x[x!=""]), collapse=",")
                })
  platetools::raw_map(x, well=rownames(plate), plate="384")
}
plateMap_all(planPlate)

Source plate layout

The ink will be transferred from a source plate in 384-well format. There needs more green ink for the leaves than red and brown ink for the balls and the stem, so there will be more than one well containing green ink.

colSums(as.data.frame(planPlate)[,c("stem", "leaves", "balls")], na.rm = TRUE)
#>   stem leaves  balls 
#>   8000 127000   7000
sourcePlate <- Plate("384", deadVolume = 1e4, maxVolume = 1e5)
sourcePlate <- sourcePlate |>
  set_block(  "A01",   "stem",   20000) |>
  set_block("A02~A04", "leaves", 60000) |>
  set_block(  "A05",   "balls",  20000)
plateMap_all(sourcePlate)

Plan the transfer

Next, let’s plan the transfer!

destPlate   <- Plate("384", deadVolume = 1e4, maxVolume = 1e5)

echo <- planTransfers(sourcePlate, destPlate, planPlate)
echo
#> A 525 Echo machine:
#>   Source plate:      A Plate with data about 384 wells (dead volume: 10000; max volume: 1e+05).
#>   Destination plate: A Plate with data about 384 wells (dead volume: 10000; max volume: 1e+05).
#> Transducer at the following coordinates:
#>   Source:      A05
#>   Destination: M16
#> 142 elements in the log.
transfers <- showLogs(echo)
head(transfers)
#>   from  to  vol what
#> 1  A01 H21 1000 stem
#> 2  A01 H22 1000 stem
#> 3  A01 H23 1000 stem
#> 4  A01 H24 1000 stem
#> 5  A01 I21 1000 stem
#> 6  A01 I22 1000 stem
## We can export the transfer log as a CSV file to be loaded in the Echo machine.
# write.table( exportLogs(echo), file = "Xmas.csv"
#            , quote = FALSE, row.names = FALSE, col.names = TRUE, sep = ",")