qc_violin_plot {bulkAnalyseR}

Create a violin/box plot of expression across samples of an experiment

Description

This function creates a combined violin and box plot between all samples in the expression matrix. Metadata columns are used to colour samples.

Usage

qc_violin_plot(
  expression.matrix,
  metadata,
  annotation.id,
  log.transformation = TRUE
)

Arguments

expression.matrix

the expression matrix; rows correspond to genes and columns correspond to samples; usually preprocessed by preprocessExpressionMatrix; a list (of the same length as modality) can be provided if #' length(modality) > 1

metadata

a data frame containing metadata for the samples contained in the expression.matrix; must contain at minimum two columns: the first column must contain the column names of the expression.matrix, while the last column is assumed to contain the experimental conditions that will be tested for differential expression; a list (of the same length as modality) can be provided if #' length(modality) > 1

annotation.id

name of metadata column on which to group samples

log.transformation

whether expression should be shown on log (default) or linear scale

Value

The violin/box plot as a ggplot object.

Examples

expression.matrix.preproc <- as.matrix(read.csv(
  system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"), 
  row.names = 1
))[1:500,]

metadata <- data.frame(
  srr = colnames(expression.matrix.preproc), 
  timepoint = rep(c("0h", "12h", "36h"), each = 2)
)
print(qc_violin_plot(expression.matrix.preproc, metadata, 'timepoint'))