SPADE.flattenAnnotations: Flatten list of annotations to matrix

In olimora/mySPADE: SPADE -- An analysis and visualization tool for Flow Cytometry

Description

Helper function for flattening list of annotations

Usage

SPADE.flattenAnnotations(annotations)

Arguments

annotations

A list of annotation matrices. All matrices must have the same number of rows.

Value

Single matrix of annotations

Author(s)

Michael Linderman

Examples

	# Not run
	## Load two-parameters sample data included in package
	#data_file_path = paste(installed.packages()["spade","LibPath"],"spade","extdata","SimulatedRawData.fcs",sep=.Platform$file.sep)

	## Run basic SPADE analyses, clustering on two parameters. 
	#output_dir <- tempdir()
	#SPADE.driver(data_file_path, out_dir=output_dir, cluster_cols=c("marker1","marker2"))

	## Compute medians, counts and other parameters from processed files
	#upsampled_file_path <- paste(output_dir,.Platform$file.sep,basename(data_file_path),".density.fcs.cluster.fcs",sep="")
	#mst_graph <- igraph:::read.graph(paste(output_dir,"mst.gml",sep=.Platform$file.sep),format="gml")
	#anno <- SPADE.markerMedians(upsampled_file_path, igraph:::vcount(mst_graph), cols = c("marker1","marker2"))

	## Flatten annotations so they can easily be saved in table
	#flat_anno <- SPADE.flattenAnnotations(anno)

olimora/mySPADE documentation built on May 9, 2019, 8:09 p.m.