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

plotDRExpressionR Documentation

Show gene expression in the space of reduced dimensionality.

Description

Plot selected gene expression in reduced dimension space and save to file.

Usage

plotDRExpression(
  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,
  title
)

## S4 method for signature 'CellRouter'
plotDRExpression(
  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,
  title
)

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).

title

character; the title of the plot.

Value

ggplot2; plot.


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