splots: visualization of data from assays in microtitre plate or slide format
2021-01-04
Package
splots 1.60.0
This package is provided to support legacy code and reverse dependencies, but it should not be used as a dependency for new code development. It provides a single function, plotScreen, for visualising data in microtitre plate or slide format. As a better alternative for such functionality, please consider the platetools package (see also https://github.com/Swarchal/platetools), or generic ggplot2 graphics functionality.
Here we give a short demo. First, we load and explore some example data.
data("featuresPerWell", package = "HD2013SGI")
str(featuresPerWell[[1]])## 'data.frame': 231840 obs. of 4 variables:
## $ plate: chr "001CIQ01IRI" "001CIQ01IRI" "001CIQ01IRI" "001CIQ01IRI" ...
## $ row : chr "B" "B" "B" "B" ...
## $ col : chr "1" "1" "1" "1" ...
## $ field: chr "1" "2" "3" "4" ...str(featuresPerWell[[2]])## num [1:231840, 1:353] 2780 3120 2242 2603 2170 ...
## - attr(*, "dimnames")=List of 2
## ..$ : NULL
## ..$ : chr [1:353] "count" "nuc.0.m.cx" "nuc.0.m.cy" "nuc.0.m.majoraxis" ...stopifnot(nrow(featuresPerWell[[1]]) == nrow(featuresPerWell[[2]]))We use a subset of these data and assemble them into the list xl. The details of how this is done in the following code chunk are arcane and are likely not to matter much to you; what is important is that you bring your data into the same format.
np = 40
nx = 24
ny = 16
plateNames = unique(featuresPerWell[[1]]$plate)
assertthat::assert_that(length(plateNames) >= np)
plateNames = plateNames[seq_len(np)]
xl = lapply(plateNames, function(pl) {
sel = with(featuresPerWell[[1]], plate == pl & field == "1")
rv = rep(NA_real_, nx * ny)
r = match(featuresPerWell[[1]]$row[sel], LETTERS)
c = match(featuresPerWell[[1]]$col[sel], paste(seq_len(nx)))
i = (r-1) * nx + c
assertthat::assert_that(!any(is.na(r)), !any(is.na(c)), !any(duplicated(i)),
all(r>=1), all(r<=ny), all(c>=1), all(c<=nx))
rv[i] = featuresPerWell[[2]][sel, "count"]
rv
})
names(xl) = plateNamesSo this the object xl that is passed into plotScreen:
class(xl)## [1] "list"length(xl)## [1] 40names(xl)[1:4]## [1] "001CIQ01IRI" "002CIQ01IIRI" "003CIIQ01IRI" "004CIIQ01IIRI"unique(vapply(xl, function(x) paste(class(x), length(x)), character(1)))## [1] "numeric 384"xl[[1]][1:30]## [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## [16] NA NA NA NA NA NA NA NA NA 2780 2170 2548 2673 2486 2611splots::plotScreen(xl, nx = nx, ny = ny, ncol = 4,
fill = c("white", "darkgoldenrod4"),
main = "HD2013SGI", legend.label = "cell count",
zrange = c(0, max(unlist(xl), na.rm = TRUE)))
Figure 1: Output of splots::plotScreen
sessionInfo()## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] BiocStyle_2.22.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.7 knitr_1.36 magrittr_2.0.1
## [4] R6_2.5.1 rlang_0.4.12 fastmap_1.1.0
## [7] stringr_1.4.0 highr_0.9 tools_4.1.1
## [10] grid_4.1.1 xfun_0.27 jquerylib_0.1.4
## [13] htmltools_0.5.2 yaml_2.2.1 digest_0.6.28
## [16] assertthat_0.2.1 bookdown_0.24 BiocManager_1.30.16
## [19] RColorBrewer_1.1-2 sass_0.4.0 splots_1.60.0
## [22] codetools_0.2-18 evaluate_0.14 rmarkdown_2.11
## [25] stringi_1.7.5 compiler_4.1.1 bslib_0.3.1
## [28] magick_2.7.3 jsonlite_1.7.2