plot_protein_corrplot: Peptide correlation matrix (heatmap)

View source: R/correlation-based_diagnostics.R

plot_protein_corrplotR 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 = NULL, protein_col = "ProteinName",
  feature_id_col = "peptide_group_label",
  factors_to_plot = c("ProteinName"), cluster_rows = FALSE,
  cluster_cols = FALSE,
  heatmap_color = colorRampPalette(rev(brewer.pal(n = 7, name =
  "RdYlBu")))(100), color_list = NULL, filename = NULL, width = NA,
  height = NA, units = 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. See "example_proteome_matrix" for more details (to call the description, use help("example_proteome_matrix"))

protein_name

the name of the protein

peptide_annotation

long format data frame with peptide ID and their corresponding protein and/or gene annotations. See help("example_peptide_annotation").

protein_col

column where protein names are specified

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.

factors_to_plot

vector of technical and biological covariates to be plotted in this diagnostic plot (assumed to be present in sample_annotation)

cluster_rows

boolean values determining if rows should be clustered or hclust object

cluster_cols

boolean values determining if columns should be clustered or hclust object

heatmap_color

vector of colors used in heatmap.

color_list

list, as returned by sample_annotation_to_colors, where each item contains a color vector for each factor to be mapped to the color.

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

units

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

plot_title

title of the plot (e.g., processing step + representation level (fragments, transitions, proteins) + purpose (meanplot/corrplot etc))

...

parameters for the corrplot visualisation

Value

pheatmap object

Examples

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

protein_corrplot_plot <- plot_protein_corrplot(example_proteome_matrix, 
 protein_name = c('Haao', 'Dhtkd1'), 
 peptide_annotation = example_peptide_annotation,
 protein_col = 'Gene', factors_to_plot = 'Gene')


symbioticMe/proBatch documentation built on April 9, 2023, 11:59 a.m.