readTemplate: readTemplate

In aertslab/ScoMAP: ScoMAP: Single-Cell Omics Mapping into spatial Axes using Pseudotemporal ordering

Description

Read virtual template (in jpeg) into R. The spatially located regions must be coloured differently, and no borders should be used.

Usage

readTemplate(
  pathToImage,
  k,
  bgThr = 0.93,
  neighbours = c(20, 5),
  refineRound = 2,
  plot = TRUE
)

Arguments

pathToImage	Path to the jpeg or png image. The number of virtual cells will be determined by the size of the picture.
k	Number of spatial domains in the image
bgThr	Threshold (between 0 and 1) above which all the color channels (RGB) have to be above for the pixel to be considered background. Default:0.93
neighbours	Number of neighbours to be used to refine color cluster assignment. It must be the same length as the number of refinement rounds. Default: c(20, 5).
refineRound	Number of cluster refinement rounds. Default:2
plot	Boolean indicating whether to return the computed template colored by spatial sections. Default: TRUE.

Value

A virtual map data.frame containing the virtual cell coordinates, assigned spatial cluster (original and refined), and cluster color

Examples

virtualTemplate <- readTemplate(pathToJpeg, k=8, bgThr=0.93, neighbours=c(20,5), refineRound=2)

aertslab/ScoMAP documentation built on Oct. 8, 2021, 1:15 a.m.