neighbor_ray_plot: Plot nearest neighbor ray plots for each samples

Description Usage Arguments Value Examples

Description

Plot nearest neighbor ray plots for each samples

Usage

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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

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#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))
}

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