plot_interactions: Plot counts for many genes

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Plot counts for many genes

Description

Plot counts for many genes

Usage

plot_interactions(
  x,
  intgroups,
  ylab = "scaled rlog",
  scaled = TRUE,
  n = 40,
  max_scale,
  reorder,
  ...
)

Arguments

x	a tibble from top_counts
intgroups	two column names in attr(x, "colData") to use for grouping
ylab	y-axis label
scaled	scale counts
n	total number of genes to plot
max_scale	maximum values for scaled values in case of outliers
reorder	level names to reorder factor levels on x-axis
...	additional options like ncol or nrow passed to facet_wrap

Value

A ggplot

Author(s)

Chris Stubben

Examples

 x <- top_counts( pasilla$results, pasilla$rlog, top=25)
 # no interaction from single or paired end as expected
 plot_interactions(x,  c("condition", "type"))

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