plot_protein_corrplot {proBatch}R Documentation

Peptide correlation matrix (heatmap)

Description

Plots correlation plot of peptides from a single protein

Usage

plot_protein_corrplot(data_matrix, protein_name, peptide_annotation,
  protein_col = "ProteinName", feature_id_col = "peptide_group_label",
  flavor = c("pheatmap", "corrplot"), filename = NULL, width = NA,
  height = NA, unit = c("cm", "in", "mm"),
  plot_title = sprintf("Peptide correlation matrix of %s protein",
  protein_name), ...)

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

protein_name

the name of the protein

peptide_annotation

df with peptides and their corresponding proteins

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.

flavor

either corrplot from 'corrplot' package or heatmap, as in 'pheatmap'

filename

path where the results are saved. If null the object is returned to the active window; otherwise, the object is save into the file. Currently only pdf and png format is supported

width

option determining the output image width

height

option determining the output image width

unit

units: 'cm', 'in' or 'mm'

plot_title

The title of the plot

...

parameters for the corrplot visualisation

Value

corrplot or pheatmap object depending on flavor

Examples

protein_corrplot_plot <- plot_protein_corrplot(example_proteome_matrix, protein_name = 'Haao',
               peptide_annotation = example_peptide_annotation, 
               protein_col = 'Gene', flavor = "pheatmap")


[Package proBatch version 1.0.0 Index]