interaction_maps {IrisSpatialFeatures} | R Documentation |
Plot interaction maps for all samples
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")
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') |
plot of interactions for all samples
#' #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)