plot_single_feature {proBatch}R Documentation

Plot peptide measurements

Description

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

Usage

plot_single_feature(pep_name, df_long, sample_annotation,
  order_col = "order", sample_id_col = "FullRunName",
  batch_col = "MS_batch", measure_col = "Intensity",
  feature_id_col = "peptide_group_label", geom = c("point", "line"),
  color_by_batch = FALSE, color_scheme = "brewer",
  facet_by_batch = FALSE, color_by_col = NULL, color_by_value = NULL,
  plot_title = NULL, vline_color = "red", theme = "classic")

Arguments

pep_name

name of the peptide for diagnostic profiling

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)

order_col

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

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.

geom

whether to show the feature as points and/or connect by lines

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

vline_color

color of vertical lines, typically denoting different MS batches in ordered runs; should be NULL for experiments without intrinsic order

theme

plot theme (default is 'classical'; other options not implemented)

Value

ggplot2 type plot of measure_col vs order_col, faceted by pep_name and (optionally) by batch_col

See Also

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

Examples

single_feature_plot <- plot_single_feature(
pep_name = "46213_NVGVSFYADKPEVTQEQK_2", 
df_long = example_proteome, example_sample_annotation, 
color_by_col = NULL)


[Package proBatch version 1.0.0 Index]