plot_expression_profile: Plot expression profile of given genes across samples

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

Plot expression profile of given genes across samples

Description

Plot expression profile of given genes across samples

Usage

plot_expression_profile(
  genes,
  exp,
  metadata,
  metadata_cols = 1,
  plot_module = TRUE,
  net,
  modulename,
  bg_line = "mean"
)

Arguments

genes	Character vector containing a subset of genes from which edges will be extracted. It can be ignored if plot_module is TRUE.
exp	A gene expression data frame with genes in row names and samples in column names or a 'SummarizedExperiment' object.
metadata	A data frame of sample metadata containing sample names in row names and sample annotation in subsequent columns. Ignored if 'exp' is a 'SummarizedExperiment' object, since colData will be automatically extracted.
metadata_cols	A character or numeric scalar indicating which column should be extracted from column metadata if exp is a 'SummarizedExperiment' object. The column to be extracted can be represented by indices (numeric) or column names (character). By default, the first column is used.
plot_module	Logical indicating whether to plot a whole module or not. If set to FALSE, genes must be specified.
net	List object returned by exp2gcn.
modulename	Name of the module to plot.
bg_line	Character indicating what to show in the background (black) line. One of "mean" or "median". Default: "mean".

Value

A ggplot object showing the expression profile of some genes across all samples.

Author(s)

Fabricio Almeida-Silva

Examples

data(zma.se)
data(filt.se)
genes <- rownames(filt.se)
plot_expression_profile(genes = genes, exp = zma.se, plot_module = FALSE)

almeidasilvaf/BioNERO documentation built on Oct. 9, 2024, 1:49 a.m.