msiPlot {cytofast} | R Documentation

## Draw a density (median signal intensity) plot

### Description

Function to plot the density (median signal intensity) for given markers.

### Usage

    msiPlot(cfList, markers, byGroup = NULL, byCluster = NULL, ...)

### Arguments

`cfList` | a cfList object. It should contain at least data in the 'expr' and 'samples' slots.
`markers` | character vector with column names of the markers to be plotted. A numeric vector is also accepted, note that 1 starts after removing columns 'clusterID' and 'sampleID'.
`byGroup` | a character, referring to a column name in the `samples` slot of the `cfList`. This will be used as the grouping for the y-axis.
`byCluster` | character vector specifying which cluster to be plotted. This will be used as the grouping for the y-axis.
`...` | Additional arguments passed on to `geom_density_ridges`.

### Value

None

### Examples

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

    # relabeling of clusterID
    levels(cfData@expr[,"clusterID"]) <- gsub("[^0-9]", "", levels(cfData@expr[,"clusterID"]))

    # 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 median signal intensity plot, by group
    msiPlot(cfData, markers = c("MHC.II", "CD45", "CD4"), byGroup = 'group')

    # Or by cluster
    msiPlot(cfData, markers = c("MHC.II", "CD45", "CD4"), byCluster = c("1", "6", "10"))

[Package cytofast version 1.4.0 Index]