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Plot heatmap of hierarchically clustered sample correlations or gene expression

Source: R/exploratory_analysis.R
plot_heatmap.Rd

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().

Value

A heatmap of sample correlations or gene expression.

See also

RColorBrewer

Author

Fabricio Almeida-Silva

Examples

# \donttest{
data(filt.se)
plot_heatmap(filt.se)

# }