run.compass.once: Run COMPASS once

In seshadrilab/flowHelpers: Collection of helper functions for analyzing FCM data

Description

This function runs COMPASS once, saving output to disk. Intended for use by the generic.compass.wrapper function below.

Usage

run.compass.once(gs, cnode, individuals, nodemarkermap, iter = 40000,
  lineplotxvar = NULL, run = NULL, outdir, uniqueruns = NULL,
  grouping = NULL, lineplotgroupby = NULL, countFilterThreshold = 0,
  seed = NULL)

Arguments

gs	The GatingSet of GatingSetList
cnode	Node on which to run COMPASS
individuals	pData column containing individual identifiers (rows of heatmap)
nodemarkermap	List mapping nodes to marker names
iter	(Optional) Number of COMPASS iterations to perform on each repitition (8 repetitions total) [default 40,000]
lineplotxvar	(Optional) pData column which defines groups along x-axis in FS-score line plot, e.g. Time [default NULL]
outdir	Directory in which to save output, e.g. heatmaps
uniqueruns	(Optional) pData column identifying unique runs. Use if you need multiple runs. [default NULL]
grouping	(Optional) pData columns on which to group rows in heatmap, as a character vector [default NULL]
lineplotgroupby	(Optional) This should be specified if lineplotxvar is given. pData column which defines which values to connect in the line plot (usually something like "PTID")
seed	(Optional) Number to set seed to [default NULL]

Value

Nothing

seshadrilab/flowHelpers documentation built on May 23, 2019, 4:05 a.m.