plot_counts: Plot counts for a single gene

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Plot counts for a single gene

Description

Plot counts for a single gene

Usage

plot_counts(
  x,
  intgroup,
  n = 25,
  geom = "jitter",
  ylab = "Log2 counts",
  reorder,
  ncol = NULL,
  scales = "fixed",
  ...
)

Arguments

x	a tibble from top_counts
intgroup	column name in attr(x, "colData") to use for grouping
n	total number of genes to plot, default 25
geom	geom type, default jitter or point, boxplot and violin
ylab	y-axis label
reorder	level names to reorder factor levels on x-axis
ncol	number of columsn for facet_wrap
scales	scales for facet_wrap, default fixed
...	additional options passed to geom_jitter or other geom

Value

A ggplot

Note

See link{plot_interactions} to plot many genes.

Author(s)

Chris Stubben

Examples

 x <- top_counts(pasilla$results, pasilla$rlog, top=12)
 plot_counts(x, "condition")

HuntsmanCancerInstitute/hciR documentation built on Aug. 20, 2024, 12:22 a.m.