plot_gene: Show gene expression in relation to a covariate

In bihealth/bioshmods: What the Package Does (One Line, Title Case)

Show gene expression in relation to a covariate

Description

Show gene expression in relation to a covariate

Usage

plot_gene(
  id,
  xCovar,
  exprs,
  covar,
  annot = NULL,
  annot_id_col = "PrimaryID",
  annot_symb_col = "SYMBOL",
  groupBy = NA,
  colorBy = NA,
  symbolBy = NA,
  trellisBy = NA
)

Arguments

id	PrimaryID of the gene (usually ENSEMBL ID)
xCovar	the x covariate – column name from the covariate table
exprs	gene expression matrix to show on the y axis; rownames must be PrimaryIDs. If NULL, the rld object from the pipeline is used.
covar	the covariate data frame containing the column xCovar
annot	annotation data frame (as returned by the get_annot() function). If empty, it will be loaded.
annot_id_col	name of the column in the annot data frame which corresponds to the rownames of the expression matrix.
annot_symb_col	name of the column in the annot data frame which should be added to the title of the plot.
groupBy	name of the covariate column by which to group and connect by lines the data points
colorBy	name of the covariate column by which to color the data
symbolBy	name of the covariate column by which to select point symbols
trellisBy	name of the covariate column for use in a trellis (multipanel) plot

Value

a ggplot2 object

bihealth/bioshmods documentation built on July 1, 2023, 4:32 a.m.