plot_heatmap {BioNERO}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,
  cor_method = "spearman",
  type = "samplecor",
  palette = NULL,
  log_trans = FALSE,
  cluster_rows = TRUE,
  cluster_cols = TRUE,
  show_rownames = FALSE,
  show_colnames = TRUE,
  scale = "none",
  fontsize = 9,
  cutree_rows = NA,
  cutree_cols = NA,
  ...
)

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 2 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. Only one column is allowed to ensure legends can be visualized. Default: NA.

cor_method

Correlation method. One of 'spearman' or 'pearson'. Default is 'spearman'.

type

Type of heatmap to plot. One of 'samplecor' (sample correlations) or 'expr'. Default: 'samplecor'.

palette

RColorBrewer palette to use. Default is "Blues" for sample correlation heatmap and "YlOrRd" for gene expression heatmap.

log_trans

Logical indicating whether to log transform the expression data or not. Default: FALSE.

cluster_rows

Logical indicating whether to cluster rows or not. Default: TRUE.

cluster_cols

Logical indicating whether to cluster columns or not. Default: TRUE.

show_rownames

Logical indicating whether to show row names or not. Default: FALSE.

show_colnames

Logical indicating whether to show column names or not. Default is TRUE.

scale

Character indicating if values should be centered and scaled in rows, columns, or none. One of 'row', 'column', or 'none'. Default: 'none'.

fontsize

Base font size for the plot.

cutree_rows

Number of clusters into which rows are divided. Default: NA (no division).

cutree_cols

Number of clusters into which columns are divided. Default: NA (no division).

...

Additional arguments to be passed to ComplexHeatmap::pheatmap().

Value

A heatmap of sample correlations or gene expression.

Author(s)

Fabricio Almeida-Silva

See Also

RColorBrewer

Examples


data(filt.se)
plot_heatmap(filt.se)


[Package BioNERO version 1.0.4 Index]