markerheatmap: Marker annotated heatmap

In FerrenaAlexander/FerrenaBulkRNAseq: Pipeline for analysis of bulkRNAseq data

Marker annotated heatmap

Description

Heatmaps with annotations for samples (columns) and rows (genes), useful to plot celltype markers

Usage

markerheatmap(
  res,
  geneannots,
  metadata,
  lfc_thres,
  pval_thres,
  do.scale,
  do.log,
  legend_caption,
  drop.dup.genes,
  ...
)

Arguments

res	a data.frame. one row for each gene. first three columns must be 1) gene symbol or id; 2) fold change; and 3) pvalue or padj. rest of the columns are normalized counts.
geneannots	a data.frame. one row for each gene. first column must be gene, second column must be celltype, third column must be color for each celltype
metadata	a data.frame. sample metadata, each row s a sample. must have rownames = colnames of samples in res (ie, colnames of res[,-c(1:3)] ); must also have a column called "Condition" for each sample condition, and a column called "Color" for each sample color; if two conditions, must have two colors
lfc_thres	numeric, a cutoff for lfc to be considered significant, default is 1
pval_thres	numeric, a cutoff for pval/padj to be considered significant, default is 0.05
do.scale	T/F, whether to scale genes, default is T
do.log	T/F, whether to log1p genes, default is T
legend_caption	string, caption to use above figure legend, by default will guess based on scale/log options
drop.dup.genes	T/F whether to drop duplicated genes, by default T, if set to F and dup genes are detected will throw an error
...	additional options passed on to ComplexHeatmap::Heatmap(), see ?ComplexHeatmap::Heatmap()

FerrenaAlexander/FerrenaBulkRNAseq documentation built on Oct. 16, 2022, 8:18 a.m.