plot_single_feature {proBatch} | R Documentation |
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.
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")
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_annotation |
data matrix with:
|
order_col |
column in |
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 |
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 |
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 |
vline_color |
color of vertical lines, typically denoting
different MS batches in ordered runs; should be |
theme |
plot theme (default is 'classical'; other options not implemented) |
ggplot2 type plot of measure_col
vs order_col
,
faceted by pep_name
and (optionally) by batch_col
Other feature-level diagnostic functions: plot_iRT
,
plot_peptides_of_one_protein
,
plot_spike_in
,
plot_with_fitting_curve
single_feature_plot <- plot_single_feature( pep_name = "46213_NVGVSFYADKPEVTQEQK_2", df_long = example_proteome, example_sample_annotation, color_by_col = NULL)