plot_iRT {proBatch} | R Documentation |
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.
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", ...)
df_long |
data frame where each row is a single feature in a single
sample. It minimally has a |
sample_annotation |
data matrix with:
|
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 |
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 |
measure_col |
if |
feature_id_col |
name of the column with feature/gene/peptide/protein
ID used in the long format representation |
color_by_batch |
(logical) whether to color points by batch |
color_scheme |
color scheme for |
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 |
value in |
plot_title |
the string indicating the source of the peptides |
... |
additional arguments to |
ggplot2 type plot of measure_col
vs order_col
,
faceted by irt_pattern
containing proteins
and (optionally) by batch_col
Other feature-level diagnostic functions: plot_peptides_of_one_protein
,
plot_single_feature
,
plot_spike_in
,
plot_with_fitting_curve
irt_plot <- plot_iRT(example_proteome, example_sample_annotation, protein_col = 'Gene', irt_pattern = "BOVINE_A1ag")