ggplotCounts {ideal} | R Documentation |
Plot for normalized counts of a single gene, with jittered points superimposed on the boxplot
ggplotCounts(dds, gene, intgroup = "condition", annotation_obj = NULL, transform = TRUE)
dds |
A |
gene |
A character, specifying the name of the gene to plot |
intgroup |
Interesting groups: a character vector of
names in |
annotation_obj |
A |
transform |
Logical value, corresponding whether to have log scale y-axis or not. Defaults to TRUE. |
Note: this function relies on the plotCounts
function of DESeq2,
therefore pseudocounts of 0.5 are added to each point
An object created by ggplot
library(airway) data(airway) airway dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway), colData = colData(airway), design=~cell+dex) ggplotCounts(dds_airway, gene = "ENSG00000103196", # CRISPLD2 in the original publication intgroup = "dex")