GeneModulePheatmap: Function for plotting gene module pheatmap from Seurat object

In alexthiery/scHelper: R package containing helper functions for single cell analysis

Function for plotting gene module pheatmap from Seurat object

Description

col_ann_order can be specified to change the order in which the column annotations appear on the heatmap

Usage

GeneModulePheatmap(
  seurat_obj,
  metadata,
  col_order = metadata[1],
  custom_order = NULL,
  custom_order_column = NULL,
  assay = "RNA",
  slot = "scale.data",
  gene_modules,
  selected_genes = NULL,
  hide_annotation = NULL,
  gaps_row = TRUE,
  gaps_col = NULL,
  gm_row_annotation = TRUE,
  cell_subset = NULL,
  use_seurat_colours = TRUE,
  colour_scheme = c("PRGn", "RdYlBu", "Greys"),
  col_ann_order = rev(metadata),
  show_colnames = FALSE,
  show_rownames = TRUE,
  cluster_rows = FALSE,
  cluster_cols = FALSE,
  order_genes = TRUE,
  annotation_names_row = FALSE,
  ...
)

Arguments

seurat_obj	Seurat object
metadata	a string or array of colnames in [e-mail] used to annotate the cells.
col_order	cell order will be prioritised by the order of elements in the array. By default cells are ordered by the first element of the metadata variable.
custom_order	array specifying cell group ordering. If set then custom_order_column must also be set.
custom_order_column	metadata column from which custom_order is derived.
assay	seurat assay to use for plotting.
slot	seurat slot to use for plotting.
gene_modules	list of gene modules to plot.
selected_genes	optional array of genes to filter gene modules. Modules with no selected_genes present will be removed.
hide_annotation	array of elements to hide from column annotation.
gaps_row	boolean specifying whether to add whitespace between gene modules.
gaps_col	metadata column by which to add whitespace.
gm_row_annotation	boolean specifying whether to add gene module row annotations.
cell_subset	array of cells to subset for plotting. If specified, data will be re-scaled.
use_seurat_colours	boolean specifying whether to use default seurat colours. If FALSE, colours from colour_scheme will be used instead.
colour_scheme	array or colour schemes from RColourBrewer to be used for annotating columns.
col_ann_order	can be specified to change the order of the column annotations.
show_colnames	default parameter passed to pheatmap.
show_rownames	default parameter passed to pheatmap.
cluster_rows	default parameter passed to pheatmap.
cluster_cols	default parameter passed to pheatmap.
order_genes	boolean specifying whether to order genes within gms based on hclustering
annotation_names_row	default parameter passed to pheatmap.
...	Extra arguments to be passed to pheatmap.

Value

plot output from pheatmap.

alexthiery/scHelper documentation built on Aug. 26, 2023, 3:42 p.m.