cytoBoxplots: Draw boxplots for cfList

Description Usage Arguments Value Examples

View source: R/cytoBoxplots.R

Description

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

Usage

1

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

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# 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.