plot_sample_nas: Plot missingness per sample / subgroup

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Plot missingness per sample / subgroup

Description

plot_sample_nas shows systematic and random missingness (white), and full detection (bright color) at sample resolution. Imputations are also shown (light color).

Usage

plot_detections(...)

plot_summarized_detections(...)

plot_sample_nas(
  object,
  by = "subgroup",
  fill = by,
  palette = make_svar_palette(object, fill),
  axis.text.y = element_blank()
)

plot_subgroup_nas(
  object,
  by = "subgroup",
  fill = by,
  palette = NULL,
  na_imputes = TRUE
)

Arguments

...	used to maintain deprecated functions
object	SummarizedExperiment
by	svar (string)
fill	svar (string)
palette	color vector (names = levels, values = colors)
axis.text.y	passed to ggplot2::theme
na_imputes	TRUE or FALSE

Details

plot_subgroup_nas shows systematic missingness at subgroup resolution. Random missingness and full detection are shown together (bright color). Imputations are also shown (light color).

Value

ggplot object

Examples

file <- system.file('extdata/fukuda20.proteingroups.txt', package = 'autonomics')
object <- read_maxquant_proteingroups(file)
plot_sample_nas(object)
plot_sample_nas(impute(object))
plot_subgroup_nas(object)
plot_subgroup_nas(impute(object))

subgroups <- sprintf('%s_STD', c('E00','E01','E02','E05','E15','E30','M00'))
file <- system.file('extdata/billing19.proteingroups.txt', package = 'autonomics')
object <- read_maxquant_proteingroups(file, subgroups = subgroups)
plot_subgroup_nas(object)
plot_subgroup_nas(object, 'subgroup')
plot_sample_nas(object)
plot_sample_nas(object, 'subgroup')

bhagwataditya/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.