spatial_sample_visualization: Spatial Cell Mask Visualization

In Jerby-Lab/opipes: What the Package Does (One Line, Title Case)

Spatial Cell Mask Visualization

Description

Plots for each sample, an image of each segmented cell colored by user specified features

Usage

spatial_sample_visualization(
  seg_path,
  celltypes,
  cell2rgb,
  samplename,
  background = "black",
  outpath = "~/",
  file_prefix = "",
  cont_field = "",
  contvals = NULL
)

Arguments

seg_path	string of full path to cell segmentation map
celltypes	a list of cell labels with names of the list corresponding to cellid
cell2rgb	a dictionary that matches discrete cell label to a rgb code
samplename	string name of SMI sample
background	(default "black") background color ("black" or "white")
outpath	(default = "~/") string path to output directory
file_prefix	(default = "") string prefix of file
cont_field	the celltype for which the coloring is continuous, not discrete. names must correspond to cellid
contvals	list of the hexcolors corresponding to each cell to be plotted on continuous scale

Jerby-Lab/opipes documentation built on Oct. 7, 2022, 12:28 p.m.