plot_heatmap: Plot heatmap of hierarchically clustered sample correlations...
In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

plot_heatmap

R Documentation

Plot heatmap of hierarchically clustered sample correlations or gene expression

Description

Plot heatmap of hierarchically clustered sample correlations or gene expression

Usage

plot_heatmap(
  exp,
  col_metadata = NA,
  row_metadata = NA,
  coldata_cols = NULL,
  rowdata_cols = NULL,
  type = "samplecor",
  cor_method = "spearman",
  palette = NULL,
  log_trans = FALSE,
  ...
)

Arguments

`exp`	A gene expression data frame with genes in row names and samples in column names or a 'SummarizedExperiment' object.
`col_metadata`	A data frame containing sample names in row names and sample annotation in the subsequent columns. The maximum number of columns is 3 to ensure legends can be visualized. Ignored if 'exp' is a 'SummarizedExperiment' object, since the function will extract colData. Default: NA.
`row_metadata`	A data frame containing gene IDs in row names and gene functional classification in the first column. The maximum number of columns is 3 to ensure legends can be visualized. Default: NA.
`coldata_cols`	A vector (either numeric or character) indicating which columns should be extracted from column metadata if exp is a 'SummarizedExperiment' object. The vector can contain column indices (numeric) or column names (character). By default, all columns are used.
`rowdata_cols`	A vector (either numeric or character) indicating which columns should be extracted from row metadata if exp is a 'SummarizedExperiment' object. The vector can contain column indices (numeric) or column names (character). By default, all columns are used.
`type`	Type of heatmap to plot. One of 'samplecor' (sample correlations) or 'expr'. Default: 'samplecor'.
`cor_method`	Correlation method to use in case type is "samplecor". One of 'spearman' or 'pearson'. Default is 'spearman'.
`palette`	RColorBrewer palette to use. Default is "Blues" for sample correlation heatmaps and "YlOrRd" for gene expression heatmaps.
`log_trans`	Logical indicating whether to log transform the expression data or not. Default: FALSE.
`...`	Additional arguments to be passed to `ComplexHeatmap::pheatmap()`. These arguments can be used to control heatmap aesthetics, such as show/hide row and column names, change font size, activate/deactivate hierarchical clustering, etc. For a complete list of the options, see `?ComplexHeatmap::pheatmap()`.