ggplotCounts: Plot normalized counts for a gene

In federicomarini/ideal: Interactive Differential Expression AnaLysis

Plot normalized counts for a gene

Description

Plot for normalized counts of a single gene, with jittered points superimposed on the boxplot

Usage

ggplotCounts(
  dds,
  gene,
  intgroup = "condition",
  annotation_obj = NULL,
  transform = TRUE,
  labels_repel = TRUE
)

Arguments

dds	A DESeq2::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.

Details

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

Value

An object created by ggplot

Examples

library("airway")
data("airway", package = "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"
)

federicomarini/ideal documentation built on Dec. 21, 2024, 8:46 p.m.