MAplot {MatrixQCvis} | R Documentation

## Create a MA plot

### Description

The function creates a 2D histogram of M and A values.

### Usage

    MAplot(
      tbl,
      group = c("all", colnames(tbl)),
      plot = c("all", unique(tbl[["name"]]))
    )

### Arguments

`tbl` | 'tibble' containing the M and A values, as obtained from the 'MAvalues' function
`group` | 'character', one of 'colnames(colData(se))' ('se' used in 'MAvalues') or '"all"'
`plot` | 'character', one of 'colData(se)$name' ('se' used in 'MAvalues') or '"all"'

### Details

'MAplot' returns a 2D hex histogram instead of a classical scatterplot due to computational reasons and better visualization of overlaying points. The argument 'plot' specifies the sample (refering to 'colData(se)$name') to be plotted. If 'plot = "all"', MA values for all samples will be plotted (samples will be plotted in facets). If the number of features ('tbl$Features') is below 1000, points will be plotted (via 'geom_points'), otherwise hexagons will be plotted (via 'geom_hex').

### Value

'gg' object from 'ggplot2'

### Examples

    ## create se
    set.seed(1)
    a <- matrix(rnorm(10000), nrow = 1000, ncol = 10,
                dimnames = list(1:1000, 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)))
    rD <- data.frame(spectra = rownames(a))
    se <- SummarizedExperiment::SummarizedExperiment(assay = a,
        rowData = rD, colData = cD)

    tbl <- MAvalues(se, log2 = FALSE, group = "all")
    MAplot(tbl, group = "all", plot = "all")

[Package MatrixQCvis version 1.0.0 Index]