plot_heatmap: Plot heatmap

In vari-bbc/bbcRNA: Bulk RNA-seq workflow for VAI BBC

Description

Plot heatmap with option for splitting rows and columns and adding annotation.

Usage

plot_heatmap(
  x,
  genes = rownames(x),
  de_method = "edger",
  assay_name = "norm_log_cpm",
  gene_labels = NULL,
  coldata_annot = NULL,
  coldata_split = NULL,
  rowdata_annot = NULL,
  rowdata_split = NULL,
  clust_rows = TRUE,
  clust_cols = TRUE,
  clustering_distance_rows = "euclidean",
  clustering_distance_columns = "euclidean",
  zscores = FALSE,
  grouped = FALSE
)

Arguments

x	A BbcSE object
genes	gene IDs (rownames)
de_method	"edger" or "deseq2"
assay_name	Name of assay from the 'norm_cts' slot. Not compatible with grouped=TRUE. Option was implemented with the idea of being able to plot batch-corrected data.
gene_labels	a column name from rowData. Must contain unique values
coldata_annot	character vector of colData colnames for annotating
coldata_split	character value of colData colname for splitting
rowdata_annot	character vector of rowData colnames for annotating
rowdata_split	character value of rowData colname for splitting
clust_rows	logical for whether rows should be clustered
clust_cols	logical for whether columns should be clustered
clustering_distance_rows	see 'clustering_distance_rows' in ComplexHeatmap::Heatmap()
clustering_distance_columns	see 'clustering_distance_columns' in ComplexHeatmap::Heatmap()
zscores	logical indicating whether the expression matrix should be converted to Z-scores
grouped	logical indicating whether the mean expression per group should be shown.

Value

A Heatmap-class object.

See Also

Heatmap ComplexHeatmap book

vari-bbc/bbcRNA documentation built on Nov. 10, 2020, 11:09 p.m.