draw_barplot: Barplot for Gene Expression Percentiles

In insightsengineering/hermes: Preprocessing, analyzing, and reporting of RNA-seq data

Barplot for Gene Expression Percentiles

Description

This produces a barplot of the dichotomized gene expression counts into two or three categories based on custom defined percentiles.

Usage

draw_barplot(
  object,
  assay_name,
  x_spec,
  facet_var = NULL,
  fill_var = NULL,
  percentiles = c(1/3, 2/3)
)

Arguments

object	(AnyHermesData) input.
assay_name	(string) selects assay from input.
x_spec	(GeneSpec) gene specification for the x-axis.
facet_var	(string or NULL) optional faceting variable, taken from input sample variables.
fill_var	(string or NULL) optional fill variable, taken from input sample variables.
percentiles	(vector) lower and upper percentiles to dichotomize the gene counts into two or three categories.

Value

The ggplot barplot.

Examples

object <- hermes_data

g <- genes(object)

draw_barplot(
  object,
  assay_name = "counts",
  x_spec = gene_spec(g[1]),
  facet_var = "SEX",
  fill_var = "AGE18"
)

draw_barplot(
  object,
  assay_name = "counts",
  x_spec = gene_spec(g[1:3], colMedians, "Median"),
  facet_var = "SEX",
  fill_var = "AGE18"
)

draw_barplot(
  object,
  assay_name = "counts",
  x_spec = gene_spec(g[1:3], colMeans, "Mean"),
  facet_var = "SEX",
  fill_var = "AGE18",
  percentiles = c(0.1, 0.9)
)

insightsengineering/hermes documentation built on March 1, 2023, 5:58 a.m.