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Plot low-dimensional embeddings

Source: R/Visualization.r
LowEmbedPlot.Rd

The function LowEmbedPlot is used to visualize the low-dimensional embeddings vs cluster or batch to demonstrate the clustering performance and batch remove performance.

Usage

LowEmbedPlot(
  obj,
  item = c("cluster", "batch"),
  reduction = NULL,
  combine = TRUE,
  cols = NULL,
  layout.dim = c(1, 2),
  common.legend = TRUE,
  ...
)

# S3 method for iSCMEBObj
LowEmbedPlot(
  obj,
  item = c("cluster", "batch"),
  reduction = NULL,
  combine = TRUE,
  cols = NULL,
  layout.dim = c(1, 2),
  common.legend = TRUE,
  ...
)

# S3 method for iSCMEBResObj
LowEmbedPlot(
  obj,
  item = c("cluster", "batch"),
  reduction = NULL,
  combine = TRUE,
  cols = NULL,
  layout.dim = c(1, 2),
  common.legend = TRUE,
  ...
)

Arguments

obj

A iSCMEBObj object or a iSCMEBResObj object.

item

Which feature to be used in the plot.

reduction

The name of embeddings to be used in the plot. If reduction is null, the last added one is used for plotting.

combine

An indicator of whether plot all on a figure. If TRUE, all figures are plotted; otherwise, return a list with each plot as component. TRUE by default.

cols

A vector determine the colors used in the plot.

layout.dim

The dimension in the layout of plots when combine = TRUE.

common.legend

An indicator of whether combine the legend of multiple plots. TRUE by default.

...

Arguments passed to other methods.

Value

Return a ggplot2 object.

Return a ggplot2 object.

See also

iSCMEBObj-class, plot_scatter, plot_RGB, fit.iscmeb, iSCMEBResObj-class

Examples

data(iSCMEBObj_toy)
#> Warning: data set 'iSCMEBObj_toy' not found
library(Seurat)
p1 <- LowEmbedPlot(iSCMEBObj_toy, item="cluster", reduction="TSNE2")
p2 <- LowEmbedPlot(iSCMEBObj_toy, item="batch", reduction="TSNE2")