plot_nearest_neighbor: Plot average nearest neighbor barplots for two cell types....

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

Description

Plot average nearest neighbor barplots for two cell types. This measurement is not symmetric, so if 'from' and 'to' are switched it will result in different results. For the 'to' parameter this function allows a cell-type without '+' or '-' in the end. Indicating that the distances from the first cell-type should be calculated against both '+/-' and a paired sign rank should be calculated. For example we want to calculate the average distance between SOX10 PDL1+ melanoma cells against both CD8 PD1+ and CD8 PD1- cells, the 'CD8 PD1' would be speficified as 'to' parameter, 2 distances would be calculated for each sample and a two-sided paired signed rank test calculated to test for significant differences.

Usage

plot_nearest_neighbor(x, ...)

## S4 method for signature 'ImageSet'
plot_nearest_neighbor(x, from, to, signedrank = TRUE,
  transposed = FALSE, remove_NAs = FALSE, use_pixel = FALSE)

Arguments

x	IrisSpatialFeatures ImageSet object.
...	Additional arguments.
from	Cell-type from which the nearest neighbor is calculated.
to	Cell-type to which the nearest neighbor is calculated.
signedrank	Flag indicating whether a paired signed rank test should be calculated. (default: TRUE)
transposed	Switches 'from' and 'to' cell-type. This way the (default: FALSE)
remove_NAs	dont plot samples with less than min cells
use_pixel	show the distances in pixels or micrometers (default: FALSE)

Value

plot average nearest neighbor barplots for two cell types

Examples

#loading pre-read dataset
dataset <- IrisSpatialFeatures_data
dataset <- extract_nearest_neighbor(dataset)
p <- plot_nearest_neighbor(dataset,'CD8+ PD1+','SOX10+ PDL1')

gusef/IrisSpatialFeatures documentation built on May 6, 2019, 9:50 p.m.