Plots the overall or sample-wise distribution of all peptide intensities as a boxplot or histogram.

qc_intensity_distribution(
  data,
  sample = NULL,
  grouping,
  intensity_log2,
  plot_style
)

Arguments

data

a data frame that contains at least sample names, grouping identifiers (precursor, peptide or protein) and log2 transformed intensities for each grouping identifier.

sample

a character column in the data data frame that contains the sample name. NOTE: If the overall distribution should be returned please do not provide the name of the sample column.

grouping

a character column in the data data frame that contains the grouping variables (e.g. peptides, precursors or proteins).

intensity_log2

a numeric column in the data data frame that contains the log2 transformed intensities of each grouping identifier sample combination.

plot_style

a character value that indicates the plot type. This can be either "histogram", "boxplot" or "violin". Plot style "boxplot" and "violin" can only be used if a sample column is provided.

Value

A histogram or boxplot that shows the intensity distribution over all samples or by sample.

Examples

set.seed(123) # Makes example reproducible # Create example data data <- create_synthetic_data( n_proteins = 100, frac_change = 0.05, n_replicates = 3, n_conditions = 2, method = "effect_random" ) # Plot intensity distribution # The plot style can be changed qc_intensity_distribution( data = data, sample = sample, grouping = peptide, intensity_log2 = peptide_intensity_missing, plot_style = "boxplot" )