Plot selected genes on a wide format

Plot selected genes on a wide format

degPlotWide(counts, genes, group, metadata = NULL, batch = NULL)

Arguments

counts	DESeq2::DESeqDataSet object or expression matrix
genes	character genes to plot.
group	character, colname in colData to color points and add different lines for each level
metadata	data.frame, information for each sample. Not needed if DESeq2::DESeqDataSet given as counts.
batch	character, colname in colData to shape points, normally used by batch effect visualization

Value

ggplot showing the expresison of the genes on the x axis

Examples

data(humanGender)
library(DESeq2)
idx <- c(1:10, 75:85)
dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],
  colData(humanGender)[idx,], design=~group)
dse <- DESeq(dse)
#> using pre-existing size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
#> -- replacing outliers and refitting for 1 genes
#> -- DESeq argument 'minReplicatesForReplace' = 7 
#> -- original counts are preserved in counts(dds)
#> estimating dispersions
#> fitting model and testing
degPlotWide(dse, rownames(dse)[1:10], group = "group")