plot_protein_corrplot: Peptide correlation matrix (heatmap)

In proBatch: Tools for Diagnostics and Corrections of Batch Effects in Proteomics

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')

proBatch documentation built on Nov. 8, 2020, 4:55 p.m.