plot_proximities {IrisSpatialFeatures}R Documentation

Plot proximity analysis data

Description

Plot proximity analysis data

Usage

plot_proximities(x, ...)

## S4 method for signature 'ImageSet'
plot_proximities(x, label, ordering = NULL,
  normalize = TRUE, palette = NULL, celltype_order = NULL,
  xlim_fix = 13, topbar_cols = "darkgrey")

Arguments

x

An IrisSpatialFeatures ImageSet object

...

Additional parameters.

label

Cell-type for which the proximit profile is plotted

ordering

Ordering of the samples (Default: NULL)

normalize

Flag, should the populations of different cell-types sum up to one in each sample? (Default: TRUE)

palette

Color palette, by default it uses Spectral from RColorbrewer (Default:NULL)

celltype_order

Ordering of the cell-type. (Default: NULL)

xlim_fix

Space on the right side to show the legend (Default: 13)

topbar_cols

Color of the barplots on top (Default: 'darkgrey'

Value

plot proximity analysis

Examples


#loading pre-read dataset
dataset <- IrisSpatialFeatures_data
dataset <- extract_proximity(dataset,only_closest=TRUE,radii=25)
p <- plot_proximities(dataset,"SOX10+ PDL1-",xlim_fix=3)


[Package IrisSpatialFeatures version 1.3.0 Index]