citrus.plotClusters: Plot cluster histograms

In ParkerICI/kumquat: Identification of stratifying subpopulations in Flow Cytometry Data (based on the Citrus package)

Description

Plot expression of markers in cluster cells relative to all cells

Usage

citrus.plotClusters(
  clusterIds,
  clustersData,
  colNames = names(clustersData),
  byCluster = FALSE,
  outputDir = NULL,
  outputFile = NULL
)

Arguments

clusterIds	Vector of cluster IDs to plot
clustersData	data.frame containing the clusters data. Each row is a cell and column represents the expression of different markers (non numeric columns are dropped). The data.frame must contain a column called cellType which indicates the cluster assignments. The values in clusterIds must match the values in cellType.
colNames	Which columns of clustersData to include in the plot. The default is to include all columns in the plot
byCluster	If this is TRUE this function will generate a separate plot for each cluster, otherwise or a single plot with all the clusters. The latter option may take quite long to plot if there are several clusters
outputDir	The directory in which the plots will be written (only used if byCluster == TRUE).
outputFile	The output file the plot will be written to (only used if byCluster == FALSE). Note that this needs to be the full path to the file, as outputDir is ignored when byCluster == FALSE. If this parameter is NULL and byCluster == FALSE no file will be written (and the plot will be returned invisibly)

Value

Either NULL if byCluster == TRUE or a ggplot2 plot object otherwise

ParkerICI/kumquat documentation built on Dec. 18, 2021, 6:40 a.m.