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)

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