ggplotCounts: Plot normalized counts for a gene
In ideal: Interactive Differential Expression AnaLysis

Description Usage Arguments Details Value Examples

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,
  labels_repel = TRUE
)

`dds`	A `DESeqDataSet` object.
`gene`	A character, specifying the name of the gene to plot
`intgroup`	Interesting groups: a character vector of names in `colData(dds)` to use for grouping
`annotation_obj`	A `data.frame` object, with `row.names` as gene identifiers (e.g. ENSEMBL ids) and a column, `gene_name`, containing e.g. HGNC-based gene symbols. Optional.
`transform`	Logical value, corresponding whether to have log scale y-axis or not. Defaults to TRUE.
`labels_repel`	Logical value. Whether to use `ggrepel`'s functions to place labels; 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")