plotDRExpression2-methods: Show gene expression in the space of reduced dimensionality.

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

Show gene expression in the space of reduced dimensionality.

Description

Plot selected gene expression in reduced dimension space and save to file. Version with no title.

Usage

plotDRExpression2(
  object,
  assay.type = "RNA",
  genelist,
  reduction.type = c("tsne", "pca", "DC", "umap", "custom"),
  threshold = 2,
  dims.use = c(1, 2),
  columns = 5,
  dotsize = 1,
  alpha = 0.5
)

## S4 method for signature 'CellRouter'
plotDRExpression2(
  object,
  assay.type = "RNA",
  genelist,
  reduction.type = c("tsne", "pca", "DC", "umap", "custom"),
  threshold = 2,
  dims.use = c(1, 2),
  columns = 5,
  dotsize = 1,
  alpha = 0.5
)

Arguments

object	CellRouter object.
assay.type	character; the type of data to use.
genelist	character vector; genes to show.
reduction.type	character; the dimension reduction space to be used: pca, tsne, DC of diffusion components, umap, or custom.
threshold	numeric; threshold to rescale gene expression.
dims.use	numeric vector; dimensions to use.
columns	numeric; number of columns in the output figure.
dotsize	numeric; dot size.
alpha	numeric; transparency (between 0 and 1).

Value

ggplot2; plot.

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