plotSignatureScore-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

Show gene expression in the selected space of reduced dimensionality and save to file.

Usage

plotSignatureScore(
  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'
plotSignatureScore(
  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.