cytoHeatmaps: Draw heatmaps for cfList

In cytofast: cytofast - A quick visualization and analysis tool for CyTOF data

Description

Function to draw two heatmaps. They visualize the median intensity of the markers for the created clusters. The ordering of the clusters is based on the default hierarchical cluster analysis hclust. Note that hclust takes the data after the median intensity is calculated per cluster, thus placing the most similar clusters next to each other.

Usage

cytoHeatmaps(cfList, group, legend = FALSE)

Arguments

cfList	a cfList object.
group	one of: a character vector referring to a column name in the samples slot of the cfList. a factor indicating the grouping (x-axis) for the boxplots.
legend	logical, whether a legend should be added

Value

None

Examples

# Read Data
dirFCS <- system.file("extdata", package="cytofast")
cfData <- readCytosploreFCS(dir = dirFCS, colNames = "description")

# Add cell counts to cfList and add meta data
cfData <- cellCounts(cfData, frequency = TRUE, scale = TRUE)
meta <- spitzer[match(row.names(cfData@samples), spitzer[,"CSPLR_ST"]),]
cfData@samples <- cbind(cfData@samples, meta)

# Remove unnecessary markers
cfData@expr <- cfData@expr[,-c(3:10, 13:16, 55:59, 61:63)]

# Draw heatmaps
cytoHeatmaps(cfData, group = "group", legend = TRUE)

cytofast documentation built on Nov. 8, 2020, 5:46 p.m.