normal_nearest_neighbor: Extract the distance to each nearest neighbor for specified...

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

Description

Extract the distance to each nearest neighbor for specified cell-types, normalized by downsampling each cell-type to the same size (the smallest population from among the specified markers), calculates across all samples

Usage

normal_nearest_neighbor(data, markers, n_resamples = 500,
  minimum_cells = 50, quantiles = c(0.05, 0.25, 0.5, 0.75, 0.95),
  grouped_sample = TRUE)

## S4 method for signature 'ImageSet'
normal_nearest_neighbor(data, markers, n_resamples = 500,
  minimum_cells = 50, quantiles = c(0.05, 0.25, 0.5, 0.75, 0.95),
  grouped_sample = TRUE)

Arguments

data	IrisSpatialFeatures ImageSet object
markers	vector of marker names to use
n_resamples	number of times to resample each frame (default:500)
minimum_cells	the smallest number of cells to consider a frame (default:50)
quantiles	vector of numeric fractions to include in vector to show the mean distance calculated across resamplings (default:c(0.05,0.25,0.5,0.75,0.95))
grouped_sample	TRUE/FALSE group samples together (default:TRUE)

Value

data.frame

Examples

#loading pre-read dataset
dataset <- IrisSpatialFeatures_data
dataset <- extract_nearest_neighbor(dataset)
normal_nearest_neighbor(dataset,c("SOX10+ PDL1+","SOX10+ PDL1-"),10)

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