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"
)

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".

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

Fabricio Almeida-Silva

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