plot_CV_distr {proBatch} | R Documentation |
Plot CV distribution to compare various steps of the analysis
plot_CV_distr( df_long, sample_annotation = NULL, feature_id_col = "peptide_group_label", sample_id_col = "FullRunName", measure_col = "Intensity", biospecimen_id_col = "EarTag", batch_col = NULL, unlog = TRUE, log_base = 2, offset = 1, plot_title = NULL, filename = NULL, theme = "classic" )
df_long |
as in |
sample_annotation |
data frame with:
.
See |
feature_id_col |
name of the column with feature/gene/peptide/protein
ID used in the long format representation |
sample_id_col |
name of the column in |
measure_col |
if |
biospecimen_id_col |
column in |
batch_col |
column in |
unlog |
(logical) whether to reverse log transformation of the original data |
log_base |
base of the logarithm for transformation |
offset |
small positive number to prevent 0 conversion to |
plot_title |
title of the plot (e.g., processing step + representation level (fragments, transitions, proteins) + purpose (meanplot/corrplot etc)) |
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 |
theme |
ggplot theme, by default |
ggplot
object with the boxplot of CVs on one or several steps
CV_plot = plot_CV_distr(example_proteome, sample_annotation = example_sample_annotation, measure_col = 'Intensity', batch_col = 'MS_batch', plot_title = NULL, filename = NULL, theme = 'classic')