plotSignaturesBoxplot: Plot boxplot with gene signatures.

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

Plot boxplot with gene signatures.

Description

Plot boxplot of gene expression for the specified genes in each population.

Usage

plotSignaturesBoxplot(
  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

matrix; annotations.

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