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

In tnaake/MatrixQCvis: Shiny-based interactive data-quality exploration for omics data

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

Description

The function create_boxplot creates a boxplot per sample for the intensity/count values.

Usage

createBoxplot(
  se,
  orderCategory = colnames(colData(se)),
  title = "",
  log = 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)
log	logical, if TRUE (count/intensity) values are displayed as log 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(seq_len(100), nrow = 10, ncol = 10, 
    dimnames = list(seq_len(10), paste("sample", seq_len(10))))
a[c(1, 5, 8), seq_len(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)

createBoxplot(se, orderCategory = "name", title = "", log = TRUE, 
    violin = FALSE)

tnaake/MatrixQCvis documentation built on Nov. 4, 2024, 7:42 a.m.