plot_proximities {IrisSpatialFeatures} | R Documentation |
Plot proximity analysis data
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")
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' |
plot proximity analysis
#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)