heatmap_expression: Create heatmap of gene expression

In OliverDietrich/SeuratHelper: Helper functions to assist scRNA-seq data analysis from a Seurat object

Create heatmap of gene expression

Description

Create heatmap of gene expression

Usage

heatmap_expression(
  object = NULL,
  features = NULL,
  coldata = NULL,
  rowdata = NULL,
  rowdata_label = "group",
  order_rows = FALSE,
  remove_duplicates = FALSE,
  collapse_replicates = TRUE,
  coldata_group_max = 100,
  cells = colnames(object),
  heatmap_colors = "RdBu",
  heatmap_color_dir = -1,
  annotation_colors = NULL,
  scale = TRUE,
  assay = NULL,
  slot = "data",
  limits = c(-2, 2),
  title = "Differentially expressed genes",
  show_rownames = FALSE,
  show_colnames = FALSE,
  gaps_row = NULL,
  ...
)

Arguments

object	Seurat object
features	Character of genes to plot
coldata	Annotation for columns
rowdata	Annotation for rows
rowdata_label	Name of the row annotation
order_rows	Whether to order rows by group
remove_duplicates	Whether to remove duplicated rows
collapse_replicates	Whether to average over groups of cells
coldata_group_max	Maxiumum number of categories for each column annotation
cells	Cells to plot
heatmap_colors	Name of color scale to use (default: "RdBu")
heatmap_color_dir	Direction of heatmap color scale
annotation_colors	List of color assignments for annotations
scale	Whether to scale expression data
assay	Which assay to take expression data from
slot	Which slot of the assay to use ("data", "counts")
limits	Limits of the color scale
title	Plot title
show_rownames	Whether to show rownames
show_colnames	Whether to show colnames
gaps_row	Numeric vector specifying row gaps
...	Other parameters passed to pheatmap

OliverDietrich/SeuratHelper documentation built on Jan. 20, 2024, 2:57 a.m.