plot_peptide_corr_distribution: Create violin plot of peptide correlation distribution

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

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",
  filename = NULL,
  width = NA,
  height = NA,
  units = c("cm", "in", "mm"),
  plot_title = "Distribution of peptide correlation",
  theme = "classic"
)

plot_peptide_corr_distribution.corrDF(
  corr_distribution,
  filename = NULL,
  width = NA,
  height = NA,
  units = c("cm", "in", "mm"),
  plot_title = "Correlation of peptides",
  theme = "classic"
)

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"))
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.
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))
theme	ggplot theme, by default classic. Can be easily overriden
corr_distribution	data frame with peptide correlation distribution

Value

ggplot object (violin plot of peptide correlation)

See Also

calculate_peptide_corr_distr, ggplot

Examples

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

selected_genes = c('BOVINE_A1ag','BOVINE_FetuinB','Cyfip1')
gene_filter = example_peptide_annotation$Gene %in% selected_genes
peptides_ann = example_peptide_annotation$peptide_group_label
selected_peptides = peptides_ann[gene_filter]
matrix_test = example_proteome_matrix[selected_peptides,]
pep_annotation_sel = example_peptide_annotation[gene_filter, ]
corr_distribution = calculate_peptide_corr_distr(matrix_test, 
pep_annotation_sel, protein_col = 'Gene')
peptide_corr_distribution <- plot_peptide_corr_distribution.corrDF(corr_distribution)

## Not run: 
peptide_corr_distribution <- plot_peptide_corr_distribution.corrDF(corr_distribution, 
filename = 'test_peptide.png', 
width = 28, height = 28, units = 'cm')

## End(Not run)

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