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Boxplot for Gene Expression Values

Source: R/draw_boxplot.R
draw_boxplot.Rd

[Experimental]

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
)