write_scaffold_output: Write the result of a Scaffold analysis

In ParkerICI/scgraphs: Analyzing single-cell data using graphs

Description

This function writes the result of a Scaffold analysis. This includes both the Scaffold map itself as a graphml file, as well as (optionally) downsampled single-cell data for both the clusters and the landmarks that can be used for visualization

Usage

write_scaffold_output(
  G,
  out.dir,
  out.name,
  clusters.data = NULL,
  landmarks.data = NULL,
  downsample.to = 1000
)

Arguments

G	An igraph object representing the Scaffold map
out.dir	The name of the output directory
out.name	The name of the output Scaffold map (The extensions ".graphml" will be added to this name)
clusters.data	A data.frame containing the single-cell clustered data. Each row of this data.frame corresponds to a cell. The data.frame must contain a column called cellType indicating cluster membership for each cell. If the data was clustered with the grappolo package, this data.frame corresponds to the "all_events.rds" output file. If this is NULL no clusters data is written
landmarks.data	The landmarks data, as returned by load_landmarks or load_landmarks_from_dir If this is NULL no landmarks data is written
downsample.to	The number of events to target for downsampling, only used if either clusters.data or landmarks.data are provided

ParkerICI/scgraphs documentation built on April 30, 2021, 1:10 p.m.