cytoBoxplots: Draw boxplots for cfList

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

Description

Draw boxplots for all given clusters. Values are based on the counts slot in the cfList.

Usage

cytoBoxplots(cfList, group, stat)

Arguments

cfList	a cfList object. It should contain at least data in the 'counts' slot.
group	one of: a character referring to a column name in the samples slot of the cfList. a factor indicating the grouping (x-axis) for the boxplots.
stat	ignore, will be implemented soon.

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 boxplots
cytoBoxplots(cfData, group="group")

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