neighbor_ray_plot: Plot nearest neighbor ray plots for each samples

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

Description

Plot nearest neighbor ray plots for each samples

Usage

neighbor_ray_plot(x, ...)

## S4 method for signature 'ImageSet'
neighbor_ray_plot(x, from_type, to_type,
  from_col = "#EE7600", to_col = "#028482", format = ".pdf",
  plot_dir = "./", lineColor = "#666666", use_pixel = FALSE, height = 7,
  width = 10)

Arguments

x	An IrisSpatialFeatures ImageSet object
...	Additional arguments.
from_type	Cell type from which the rays are drawn
to_type	Cell type to which the rays are drawn
from_col	Color for the 'from' cell-type (Default: '#EE7600')
to_col	Color for the 'to' cell-type (Default: '#028482')
format	Format of the output file, can be '.pdf' or '.png' (Default: '.pdf')
plot_dir	Directory in which the images are written (Default: './')
lineColor	Color of the rays (Default: '#666666')
use_pixel	use pixels instead of micrometer for distance measurements (default: FALSE)
height	Height of the pdf. (Default: 7)
width	Width of the pdf. (Default: 10)

Value

nearest neighbor ray plots

Examples

#loading pre-read dataset
dataset <- IrisSpatialFeatures_data
dataset <- extract_nearest_neighbor(dataset)
get_nearest_neighbors(dataset,"SOX10+ PDL1+")
plot_dir <- file.path('./ray_plots')
if (!file.exists(plot_dir)){
 dir.create(file.path(plot_dir))
}

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