Make intensity boxplot

Generate boxplots of the intensity distributions for the samples in a SummarizedExperiment object.

makeIntensityBoxplots(sce, assayName, doLog, ylab, maxNGroups = 25)

Arguments

sce

A SummarizedExperiment object (or a derivative). The colData must have columns named "sample" and "group", for grouping and coloring the values, respectively.

assayName

Character scalar, the name of the assay of sce to use for the plots.

doLog

Logical scalar, whether to log-transform the y-axis.

ylab

Character scalar, the label to use for the y-axis.

maxNGroups

Numeric scalar, the maximum number of groups to display in the legend. If there are more than maxNGroups groups, the legend is suppressed.

Value

A ggplot object.

Author

Charlotte Soneson

Examples

mqFile <- system.file("extdata", "mq_example", "1356_proteinGroups.txt",
                      package = "einprot")
samples <- c("Adnp_IP04", "Adnp_IP05", "Adnp_IP06",
             "Chd4BF_IP07", "Chd4BF_IP08", "Chd4BF_IP09",
             "RBC_ctrl_IP01", "RBC_ctrl_IP02", "RBC_ctrl_IP03")
out <- importExperiment(inFile = mqFile, iColPattern = "^iBAQ\\.",
                        includeOnlySamples = samples)
sampleAnnot <- data.frame(sample = samples,
                          group = gsub("_IP.*", "", samples))
sce <- addSampleAnnots(out$sce, sampleAnnot = sampleAnnot)
makeIntensityBoxplots(sce, assayName = "iBAQ", doLog = TRUE,
                      ylab = "log intensity")
#> Warning: log-10 transformation introduced infinite values.
#> Warning: Removed 1497 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).