plotSignaturesHeatmap: Plot heatmap with gene signatures.

In edroaldo/fusca: Framework for Unified Single-Cell Analysis

Plot heatmap with gene signatures.

Description

Plot heatmap of gene expression for the specified genes in each population. The plot is not shown in the RStudio Plots display, but it is saved in the specified directory.

Usage

plotSignaturesHeatmap(
  object,
  assay.type = "RNA",
  markers,
  column.ann,
  column.color,
  num.cells = NULL,
  threshold = 2,
  genes.show = NULL,
  low = "purple",
  intermediate = "black",
  high = "yellow",
  order = NULL,
  fontsize = 5
)

Arguments

object	CellRouter object.
assay.type	character; the type of data to use.
markers	tibble; genes preferentially expressed in each column.ann, as obtained in the findSignatures function. For example, in clusters or sorted populations.
column.ann	character; column in the metadata table used to annotate the kNN graph. For example, clusters, sorted cell populations.
column.color	character; column corresponding to the colors.
num.cells	numeric; number of cells to show in the heatmap.
threshold	numeric; threshold used to center the data.
genes.show	character vector; gene names to show in the heatmap. The default is the top 5 genes according to fold change for each population.
low	character; color for low expression.
intermediate	character; color for intermediate expression.
high	character; color for high expression.
order	character vector; order of population names, the default is alphabetical order.
fontsize	numeric; font size.

Value

pheatmap; plot.

edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.