plot_heatmap {BioNERO} | R Documentation |
Plot heatmap of hierarchically clustered sample correlations or gene expression
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, ... )
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 |
A heatmap of sample correlations or gene expression.
Fabricio Almeida-Silva
data(filt.se) plot_heatmap(filt.se)