draw_boxplot: Boxplot for Gene Expression Values

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

Boxplot for Gene Expression Values

Description

This produces boxplots of the gene expression values of a single gene, multiple genes or a gene signature.

Usage

draw_boxplot(
  object,
  assay_name,
  genes,
  x_var = NULL,
  color_var = NULL,
  facet_var = NULL,
  violin = FALSE,
  jitter = FALSE
)

h_draw_boxplot_df(object, assay_name, genes, x_var, color_var, facet_var)

Arguments

object	(AnyHermesData) input.
assay_name	(string) selects assay from input for the y-axis.
genes	(GeneSpec) for which genes or which gene signature to produce boxplots.
x_var	(string or NULL) optional stratifying variable for the x-axis, taken from input sample variables.
color_var	(string or NULL) optional color variable, taken from input sample variables.
facet_var	(string or NULL) optional faceting variable, taken from input sample variables.
violin	(flag) whether to draw a violin plot instead of a boxplot.
jitter	(flag) whether to add jittered original data points.

Value

The ggplot boxplot.

Functions

• h_draw_boxplot_df(): Helper function to prepare the data frame required for plotting.

Examples

object <- hermes_data
draw_boxplot(
  object,
  assay_name = "counts",
  genes = gene_spec(c(A = genes(object)[1])),
  violin = TRUE
)

object2 <- object %>%
  add_quality_flags() %>%
  filter() %>%
  normalize()
draw_boxplot(
  object2,
  assay_name = "tpm",
  x_var = "SEX",
  genes = gene_spec(setNames(genes(object2)[1:10], 1:10), fun = colMeans),
  facet_var = "RACE",
  color_var = "AGE18",
  jitter = TRUE
)

draw_boxplot(
  object,
  assay_name = "counts",
  x_var = "SEX",
  genes = gene_spec(genes(object)[1:3]),
  jitter = TRUE,
  facet_var = "AGE18"
)

draw_boxplot(
  object,
  assay_name = "counts",
  genes = gene_spec(c(A = "GeneID:11185", B = "GeneID:10677")),
  violin = TRUE
)

insightsengineering/hermes documentation built on Sept. 19, 2024, 9:06 p.m.