Plot Individual Genes

Plot Individual Genes

# S4 method for bcbioRNASeq
plotGene(object, interestingGroups,
  normalized = "tpm", gene, format = "symbol",
  color = scale_color_viridis(discrete = TRUE), returnList = FALSE)

Arguments

object

Object.
interestingGroups

Category to use to group samples. In the plotting functions, this will define color and shape, where applicable. If unset, this is automatically determined by the metadata set inside the bcbioRNASeq object. When set to NULL, this will default to sampleName.
normalized

Normalization method. Supports tpm (default), tmm, rlog, or vst.
gene

Gene identifier. Can input multiple genes as a character vector.
format

Ensembl identifier format. Supports symbol (default) or ensgene.
color

Desired ggplot color scale. Defaults to viridis::scale_color_viridis(). Must supply discrete values. When set to NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual().
returnList

Return the plotlist used to generate the paneled, multi-gene plot with cowplot::plot_grid().

Value

See also

DESeq2::plotCounts().

Other Quality Control Plots: plot53Bias, plotCountDensity, plotCountsPerGene, plotExonicMappingRate, plotGenderMarkers, plotGeneSaturation, plotGenesDetected, plotIntronicMappingRate, plotMappedReads, plotMappingRate, plotRRNAMappingRate, plotTotalReads

Examples

# Gene symbols
symbol <- rowData(bcb)[["symbol"]][1:3]
print(symbol)
#> [1] "Rgs20" "Rab23" "Ncoa2"
plotGene(bcb, gene = symbol, format = "symbol")

# Gene identifiers

# NOT RUN {
ensgene <- rowData(bcb)[["ensgene"]][1:3]
print(ensgene)
plotGene(bcb, gene = ensgene, format = "ensgene")
# }