plot_peptide_corr_distribution {proBatch}R Documentation

Plot distribution of peptide correlations within one protein and between proteins

Description

Plot distribution of peptide correlations within one protein and between proteins

Usage

plot_peptide_corr_distribution(data_matrix, peptide_annotation,
  protein_col = "ProteinName", feature_id_col = "peptide_group_label",
  plot_title = "Distribution of peptide correlation",
  theme = "classic")

Arguments

data_matrix

features (in rows) vs samples (in columns) matrix, with feature IDs in rownames and file/sample names as colnames. Usually the log transformed version of the original data

peptide_annotation

long format data with peptide ID and their corresponding protein annotations

protein_col

the column name in peptide_annotation with protein names

feature_id_col

name of the column with feature/gene/peptide/protein ID used in the long format representation df_long. In the wide formatted representation data_matrix this corresponds to the row names.

plot_title

Title of the plot, usually processing step

theme

ggplot theme, by default classic. Can be easily overriden

...

parameters for the ggplot visualisation

Value

ggplot type object with violin plot for each plot_param

Examples

peptide_corr_distribution <- plot_peptide_corr_distribution(
example_proteome_matrix, 
example_peptide_annotation, protein_col = 'Gene')


[Package proBatch version 1.0.0 Index]