plotValue-methods: Show any numeric value in the CellRouter metadata table in...

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

Show any numeric value in the CellRouter metadata table in the space of reduced dimensionality.

Description

Show any numeric value in the CellRouter metadata table (number of detected genes, etc.) in the selected space of reduced dimensionality and save to file.

Usage

plotValue(
  object,
  assay.type = "RNA",
  variable.show,
  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'
plotValue(
  object,
  assay.type = "RNA",
  variable.show,
  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.
variable.show	character vector; values 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; the number of 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.