plot_interactions: Interaction summary plot for all cell-types and all samples...

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

Description

Interaction summary plot for all cell-types and all samples in a dataset

Usage

plot_interactions(x, ...)

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

Arguments

x	IrisSpatialFeatures ImageSet object to be plotted
...	Additional arguments
label	The cell type the interaction profile should be plotted for
ordering	Ordering of the samples (default: NULL)
normalize	Normalize the interactions with a given cell-type, so they sum up to 1 (default: TRUE)
palette	Color palette for all the cell-types (default: Spectral scheme from RColorbrewer)
celltype_order	Order in which the cell-types are displayed. (default: Alphabethically)
xlim_fix	Whitespace on the right side so the legend can be displayed clearly. (default: 13)
topbar_cols	Color of the barplots that are shown on top. (default: 'darkgrey')

Value

plot of all cell-types and samples interactions

Examples

#loading pre-read dataset
dataset <- IrisSpatialFeatures_data
dataset <- extract_interactions(dataset)
plot_interactions(dataset,'SOX10+ PDL1+',xlim_fix=3)

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