mosaic {MatrixQCvis}

R Documentation

Mosaic plot for two factors in colData(se)

Description

The function 'mosaic' creates a mosaic plot of two factors from an 'SummararizedExperiment' object. The columns 'f1' and 'f2' are taken from 'colData(se)'.

Usage

mosaic(se, f1, f2)

Arguments

se	'SummarizedExperiment' object
f1	'character', 'f1' is one of the column names in 'colData(se)'
f2	'character', 'f2' is one of the column names in 'colData(se)'

Details

Code partly taken from https://stackoverflow.com/questions/21588096/pass-string-to-facet-grid-ggplot2

Value

'gg' object from 'ggplot2'

Examples

## create se
set.seed(1)
a <- matrix(rnorm(100), nrow = 10, ncol = 10,
            dimnames = list(1:10, paste("sample", 1:10)))
a[c(1, 5, 8), 1:5] <- NA
cD <- data.frame(name = colnames(a), 
    type = c(rep("1", 5), rep("2", 5)),
    cell_type = c("A", "B"))
rD <- data.frame(spectra = rownames(a))
se <- SummarizedExperiment::SummarizedExperiment(assay = a, 
    rowData = rD, colData = cD)

mosaic(se, "cell_type", "type")

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