plot_detects {autonomics}R Documentation

Plot detections

Description

Plot detections

Usage

plot_detects(...)

plot_detections(object, subgroup = subgroup, fill = !!enquo(subgroup))

plot_quantifications(...)

plot_summarized_detections(
  object,
  subgroup = subgroup,
  fill = !!enquo(subgroup),
  na_imputes = TRUE
)

Arguments

...

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

Details

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)

Value

ggplot object

Examples

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)

[Package autonomics version 1.2.0 Index]