plot_densities: Plot sample/feature distributions

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Plot sample/feature distributions

Description

Plot sample/feature distributions

Usage

plot_densities(
  object,
  assay = assayNames(object)[1],
  group,
  fill,
  color = NULL,
  linetype = NULL,
  facet = NULL,
  nrow = NULL,
  ncol = NULL,
  dir = "h",
  scales = "free_y",
  labeller = label_value,
  palette = NULL,
  fixed = list(alpha = 0.8, na.rm = TRUE)
)

plot_sample_densities(
  object,
  assay = assayNames(object)[1],
  group = "sample_id",
  fill = if ("subgroup" %in% svars(object)) "subgroup" else "sample_id",
  color = NULL,
  linetype = NULL,
  n = 100,
  facet = NULL,
  nrow = NULL,
  ncol = NULL,
  dir = "h",
  scales = "free_y",
  labeller = label_value,
  palette = NULL,
  fixed = list(alpha = 0.8, na.rm = TRUE)
)

plot_feature_densities(
  object,
  assay = assayNames(object)[1],
  fill = "feature_id",
  group = fill,
  color = NULL,
  linetype = NULL,
  n = 9,
  facet = NULL,
  nrow = NULL,
  ncol = NULL,
  dir = "h",
  scales = "free",
  labeller = label_value,
  palette = NULL,
  fixed = list(alpha = 0.8, na.rm = TRUE)
)

Arguments

object	SummarizedExperiment
assay	string
group	svar (string)
fill	svar (string)
color	svar (string)
linetype	svar (string)
facet	svar (character vector)
nrow	number of facet rows
ncol	number of facet cols
dir	'h' (horizontal) or 'v' (vertical)
scales	'free', 'fixed', 'free_y'
labeller	e.g. label_value
palette	named character vector
fixed	fixed aesthetics
n	number

Value

ggplot object

See Also

plot_sample_violins, plot_sample_boxplots

Examples

# Data
    file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
    object <- read_metabolon(file)
    object %<>% extract(, order(.$subgroup))
    
# Sample distributions
    plot_sample_densities(object)
    plot_sample_violins(  object, facet = 'Time')
    plot_sample_boxplots(object)
    plot_exprs(object)
    plot_exprs(object, dim = 'samples', x = 'subgroup', facet = 'Time')
    
# Feature distributions
    plot_feature_densities(object)
    plot_feature_violins(  object)
    plot_feature_boxplots( object)

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