plot_proximities: Plot proximity analysis data

In gusef/Iris: A package to extract spatial features based on multiplex IF images

Description

Plot proximity analysis data

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")

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'
x	An IrisSpatialFeatures ImageSet object
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'
...	Additional parameters.

Value

plot proximity analysis

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)


#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)

gusef/Iris documentation built on May 14, 2019, 2:42 p.m.