Barplot for Gene Expression Percentiles

Source: R/draw_barplot.R

[Experimental]

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

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)
)