plotDR {CATALYST}R Documentation

Plot dim. reduction from a daFrame

Description

Plot cell-level reduced dimensions stored within a daFrame object.

Usage

plotDR(x, ...)

## S4 method for signature 'daFrame'
plotDR(x, dr = c("TSNE", "PCA", "MDS", "UMAP",
  "DiffusionMap"), color_by = "meta20", facet = NULL)

Arguments

x

a daFrame.

...

optional arguments.

dr

character string specifying the dimensionaly reduction method.

color_by

character string specifying a clustering, marker, or rowData column name to color by.

facet

a character string specifying a rowData column to facet by.

Value

a ggplot object.

Author(s)

Helena L. Crowell helena.crowell@uzh.ch

Examples

data(PBMC_fs, PBMC_panel, PBMC_md)
daf <- daFrame(PBMC_fs, PBMC_panel, PBMC_md)

daf <- runDR(daf, "PCA")
plotDR(daf, "PCA", color_by = "condition")

daf <- cluster(daf)
plotDR(daf, "PCA", color_by = "meta5")
[Package CATALYST version 1.8.7 Index]