Heatmap: Generate heatmap for the enrichment scores

In guokai8/scGSVA: GSVA and UCell signature enrichment analysis for single cell RNA seq

Generate heatmap for the enrichment scores

Description

Generate heatmap for the enrichment scores

Usage

Heatmap(
  object,
  features = NULL,
  group_by = NULL,
  color = NULL,
  scale = "row",
  average = FALSE,
  order_by = NULL,
  decreasing = FALSE,
  fontsize_row = 5,
  fontsize_col = 5,
  border_color = "grey60",
  annotation_col = NULL,
  annotation_colors = NULL,
  cluster_rows = TRUE,
  cluster_cols = TRUE,
  show_rownames = TRUE,
  show_colnames = TRUE,
  ...
)

Arguments

object	A GSVA objectect or data.frame
features	A vector of features to plot
group_by	Name of one or more metadata columns to group (color) cells by
color	vector of colors used in heatmap.
scale	character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are "row", "column" and "none"
average	use the average enrichment score or not (default: FALSE)
order_by	a charcter indicate the top of heatmap should order, only work when cluster_col = FALSE
decreasing	logical. Should the sort order be increasing or decreasing?
fontsize_row	fontsize for rownames (Default: fontsize)
fontsize_col	fontsize for colnames (Default: fontsize)
border_color	color of cell borders on heatmap, use NA if no border should be drawn.
annotation_col	data frame that specifies the annotations shown on top side of the heatmap.
annotation_colors	ist for specifying annotation_row and annotation_col track colors manually. It is possible to define the colors for only some of the features.
cluster_rows	boolean values determining if rows should be clustered or hclust object,
cluster_cols	boolean values determining if columns should be clustered or hclust object.
show_rownames	boolean specifying if column names are be shown.
show_colnames	boolean specifying if column names are be shown.
...	parameters used in pheatmap set.seed(123) library(scGSVA) data(pbmc_small) hsko<-buildAnnot(species="human",keytype="SYMBOL",anntype="KEGG") res<-scgsva(pbmc_small,hsko) Heatmap(res,group="groups")

Author(s)

Kai Guo

guokai8/scGSVA documentation built on Nov. 15, 2024, 12:54 a.m.