plot_gene {RNAseqQC}

Plot a gene

Description

Plot a gene

Usage

plot_gene(
  gene,
  dds,
  x_var = NULL,
  color_by = NULL,
  point_alpha = 0.7,
  point_rel_size = 2,
  show_plot = TRUE
)

Arguments

gene

A gene ID or gene name, i.e. an element of rownames(dds) or of rowData(dds)$gene_name

dds

a DESeqDataSet

x_var

Variable to plot on the x-axis. If NULL, then each sample is plotted separately.

color_by

Variable (column in colData(dds)) to color points by.

point_alpha

alpha value of geom_point()

point_rel_size

relative size of geom_point()

show_plot

Whether to show the plot or not

Value

The function displays the plot and returns invisible the data frame of expression values and colData annotation for the gene.

Examples

library("DESeq2")
set.seed(1)
dds <- makeExampleDESeqDataSet()
colData(dds)$type <- c("A","A","A","B","B","B")
colData(dds)$patient <- c("1","1","2","2","3","3")
dds <- estimateSizeFactors(dds)
plot_gene("gene1", dds)
plot_gene("gene1", dds, x_var="patient", color_by="type")