plotGeneViolin: Plot genes from a DESeq2 object using a violin plot
In scfurl/seqGlue: Makes sequencing data come together like glue

plotGeneViolin

R Documentation

Plot genes from a DESeq2 object using a violin plot

Description

Plot genes from a DESeq2 object using a violin plot

Usage

plotGeneViolin(
  obj,
  gene,
  intgroup = "condition",
  normalized = TRUE,
  text_size = 4,
  transform = TRUE,
  main,
  xlab = "group",
  returnData = FALSE,
  replaced = FALSE,
  gene_short_name = "gene_short_name",
  ENSID = "gene_id",
  pc,
  theme_opts = F,
  annotate_data = F,
  annotation_col = "sample",
  point_size = 6,
  colors = NULL
)

Arguments

`obj`	input object
`gene`	gene input
`intgroup`	factor to be used for grouping,
`normalized`	normalize data (default is TRUE)
`transform`	transform data (default is FALSE)
`main`	title
`xlab`	label for x axis of plot
`returnData`	return data instead of plot
`replaced`	= FALSE
`gene_short_name`	column containin gene symbol; default = "gene_short_name"
`ENSID`	column containing gene id (ENSEMBL) default = "GENEID"
`pc`	pseudocount
`theme_opts`	use theme_opts (default is T)
`annotate_data`	default F
`annotation_col`	the column of meta data to use for annotation (default ="sample")
`point_size`	default 3
`colors`	colors to use