spatial.clusters: Visualize spatial distribution of clusters.

In ludvigla/spaceST: spaceST

Description

Visualize spatial distribution of clusters.

Usage

spatial.clusters(object, clusters = NULL, HE.list = NULL,
  arrange = T, ncols = NULL, xlim = c(1, 33), ylim = c(1, 35),
  cols = NULL, ...)

Arguments

object	Object of class spaceST.
clusters	Integer/numeric vector specifying clusters.
HE.list	List of paths to HE images in jpeg format that should be used as a background for the spatial heatmap.
arrange	Arrange plots.
ncols	Number of columns in arranged plot table.
xlim, ylim	Set limits of x/y axes. [default: xlim = c(1, 34), ylim = c(1, 36)]
cols	Set custom cluster colors by specifying a character vector with color codes. You can specify specific colors for each cluster by naming the character vector with the cluster ids.
...	additional parameters passed to geom_point(), defining the attributes of the feature coordinate points.

Value

Plot of clustered featured overlayed on black and white HE image.

ludvigla/spaceST documentation built on May 29, 2019, 3:43 a.m.