create_boxplot {MatrixQCvis} | R Documentation

## Create a boxplot of (count/intensity) values per sample

### Description

The function 'create_boxplot' creates

### Usage

    create_boxplot(
      se,
      orderCategory = colnames(colData(se)),
      title = "",
      log2 = TRUE,
      violin = FALSE
    )

### Arguments

`se` | 'SummarizedExperiment' containing the (count/intensity) values in the 'assay' slot
`orderCategory` | 'character', one of 'colnames(colData(se))'
`title` | 'character' or 'numeric' of 'length(1)'
`log2` | 'logical', if 'TRUE' (count/intensity) values are displayed as log2 values
`violin` | 'logical', if 'FALSE' a boxplot is created, if 'TRUE' a violin plot is created

### Details

Internal usage in 'shinyQC'.

### Value

'gg' object from 'ggplot2'

### Examples

    ## create se
    a <- matrix(1:100, nrow = 10, ncol = 10,
        dimnames = list(1:10, paste("sample", 1:10)))
    a[c(1, 5, 8), 1:5] <- NA
    set.seed(1)
    a <- a + rnorm(100)
    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)

    create_boxplot(se, orderCategory = "name", title = "", log2 = TRUE,
        violin = FALSE)

[Package MatrixQCvis version 1.2.4 Index]