interaction_maps: Plot interaction maps for all samples

In IrisSpatialFeatures: A package to extract spatial features based on multiplex IF images

Description

Plot interaction maps for all samples

Usage

interaction_maps(x, ...)

## S4 method for signature 'ImageSet'
interaction_maps(x, int_markers, int_marker_cols,
  silent_markers = c(), silent_col = c(), outline_transparency = 0.9,
  use_dapi = FALSE, outdir = "interaction_maps", useMask = NULL,
  format = ".png")

Arguments

x	An IrisSpatialFeatures ImageSet object
...	Additional arguments.
int_markers	Cell-types that should be considered. If two cells from different cell-types interact they are filled in, if a cell is not interacting it is just outlined.
int_marker_cols	Colors for the cell-types
silent_markers	Cell-types that should only be outlined (Default: c())
silent_col	Colors for silent markers (Default: c())
outline_transparency	Dimming factor for the outlines cells(Default: 0.9)
use_dapi	Use the DAPI channel as a background (Default: FALSE)
outdir	Output directory (Default: './interaction_maps')
useMask	(Default: NULL)
format	Output format of the images. Can be '.png' or '.tiff' (Default: '.png')

Value

plot of interactions for all samples

Examples

#' #loading pre-read dataset
dataset <- IrisSpatialFeatures_data
dataset <- extract_interactions(dataset)
get_interactions(dataset,'CD8+ PD1+')
int_markers <- c('CD8+ PD1+','SOX10+ PDL1+')
int_marker_cols <- c('#dd1c77','#99d8c9')
silent_markers <- c('CD8+ PD1-')
silent_col=c('yellow')
p <- interaction_maps(dataset,int_markers,int_marker_cols,silent_markers,
                      silent_col)

IrisSpatialFeatures documentation built on May 2, 2018, 2:49 a.m.