plot_iRT {proBatch}R Documentation

Plot iRT measurements

Description

Creates a iRT facetted ggplot2 plot of the value in measure_col vs order_col using plot_single_feature. Additionally, the resulting plot can also be facetted by batch.

Usage

plot_iRT(df_long, sample_annotation, peptide_annotation = NULL,
  protein_col = "ProteinName", order_col = "order",
  irt_pattern = "iRT", sample_id_col = "FullRunName",
  batch_col = "MS_batch", measure_col = "Intensity",
  feature_id_col = "peptide_group_label", color_by_batch = FALSE,
  color_scheme = "brewer", facet_by_batch = FALSE,
  color_by_col = NULL, color_by_value = NULL,
  plot_title = "iRT peptide profile", ...)

Arguments

df_long

data frame where each row is a single feature in a single sample. It minimally has a sample_id_col, a feature_id_col and a measure_col, but usually also an m_score (in OpenSWATH output result file)

sample_annotation

data matrix with:

  1. sample_id_col (this can be repeated as row names)

  2. biological covariates

  3. technical covariates (batches etc)

peptide_annotation

long format data with peptide ID and their corresponding protein annotations

protein_col

column where protein names are specified

order_col

column in sample_annotation that determines sample order. It is used for certain diagnostics and normalisations.

irt_pattern

substring used to identify irts proteins in the column 'ProteinName'

sample_id_col

name of the column in sample_annotation file, where the filenames (colnames of the data matrix are found)

batch_col

column in sample_annotation that should be used for batch comparison

measure_col

if df_long is among the parameters, it is the column with expression/abundance/intensity; otherwise, it is used internally for consistency

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.

color_by_batch

(logical) whether to color points by batch

color_scheme

color scheme for ggplot representation

facet_by_batch

(logical) whether to plot each batch in its own facet

color_by_col

column to color by certain value denoted by color_by_value

color_by_value

value in color_by_col to color

plot_title

the string indicating the source of the peptides

...

additional arguments to plot_single_feature function

Value

ggplot2 type plot of measure_col vs order_col, faceted by irt_pattern containing proteins and (optionally) by batch_col

See Also

Other feature-level diagnostic functions: plot_peptides_of_one_protein, plot_single_feature, plot_spike_in, plot_with_fitting_curve

Examples

irt_plot <- plot_iRT(example_proteome, 
example_sample_annotation, 
protein_col = 'Gene', irt_pattern = "BOVINE_A1ag")


[Package proBatch version 1.0.0 Index]