plot_subgroup_points: Plot features

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Plot features

Description

Plot features

Usage

plot_subgroup_points(
  object,
  subgroup = "subgroup",
  block = NULL,
  x = subgroup,
  color = subgroup,
  group = block,
  facet = "feature_id",
  nrow = NULL,
  scales = "free_y",
  ...,
  palette = NULL,
  fixed = list(na.rm = TRUE),
  theme = list(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))
)

Arguments

object	SummarizedExperiment
subgroup	subgroup svar
block	block svar
x	svar mapped to x
color	svar mapped to color
group	svar mapped to group
facet	svar mapped to facets
nrow	number of rows
scales	'free_y' etc.
...	mapped aesthetics
palette	color palette (named character vector)
fixed	fixed aesthetics
theme	ggplot theme specifications

Value

ggplot object

Examples

file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
object <- read_metabolon(file, fit = 'limma')
idx <- order(fdata(object)$`p~t1-t0~limma`)[1:9]
object %<>% extract(idx, )
plot_sample_boxplots(  object)
plot_feature_boxplots( object)
plot_sample_boxplots(object, x = 'Time')
plot_subgroup_points(  object, subgroup = 'Time')
plot_subgroup_points(  object, subgroup = 'Time', block = 'Subject')

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