cytoHeatmaps {cytofast} | R Documentation

## Draw heatmaps for cfList

### 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)

[Package cytofast version 1.4.0 Index]