plot_detects {autonomics} | R Documentation |
Plot detections
plot_detects(...) plot_detections(object, subgroup = subgroup, fill = !!enquo(subgroup)) plot_quantifications(...) plot_summarized_detections( object, subgroup = subgroup, fill = !!enquo(subgroup), na_imputes = TRUE )
... |
for backward compatibilty |
object |
SummarizedExperiment |
subgroup |
subgroup var (sym) |
fill |
fill var (sym) |
na_imputes |
whether to NA imputes prior to plottin (TRUE/FALSE)g |
plot_detections
plots feature x sample detections. It shows per
feature/sample nondetects (white), imputes (light colored), and detects
(full color).
plot_summarized_detections
gives an summarized view, plotting
featuretype x subgroup detections. It visualizes the subgroup-wise nondetect
structure often seen in mass spectrometry proteomics data (across e.g.
different cell types)
ggplot object
require(magrittr) file <- download_data('fukuda20.proteingroups.txt') object <- read_proteingroups(file, impute=FALSE, plot = FALSE) plot_summarized_detections(object) plot_detections(object) plot_detections(impute_systematic_nondetects(object, plot=FALSE)) file <- download_data('halama18.metabolon.xlsx') object <- read_metabolon(file, impute = FALSE, plot = FALSE) plot_summarized_detections(object, Group) plot_detections(object, Group)