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
)

Arguments

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.

Value

An object created by ggplot

Details

Note: this function relies on the plotCounts function of DESeq2, therefore pseudocounts of 0.5 are added to each point

Examples

library(airway) data(airway) airway
#> class: RangedSummarizedExperiment #> dim: 64102 8 #> metadata(1): '' #> assays(1): counts #> rownames(64102): ENSG00000000003 ENSG00000000005 ... LRG_98 LRG_99 #> rowData names(0): #> colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521 #> colData names(9): SampleName cell ... Sample BioSample
dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway), colData = colData(airway), design = ~ cell + dex ) ggplotCounts(dds_airway, gene = "ENSG00000103196", # CRISPLD2 in the original publication intgroup = "dex" )