plot_violins {autonomics}R Documentation

Plot sample/feature violins

Description

Plot sample/feature violins

Usage

plot_violins(
  object,
  x,
  fill,
  color = NULL,
  group = NULL,
  facet = NULL,
  highlight = NULL,
  fixed = list(na.rm = TRUE)
)

plot_sample_violins(
  object,
  x = sample_id,
  fill = sample_id,
  color = NULL,
  highlight = NULL,
  fixed = list(na.rm = TRUE)
)

plot_feature_violins(
  object,
  x = feature_id,
  fill = feature_name,
  color = NULL,
  highlight = NULL,
  fixed = list(na.rm = TRUE)
)

plot_subgroup_violins(
  object,
  subgroup,
  x = !!enquo(subgroup),
  fill = !!enquo(subgroup),
  color = NULL,
  highlight = NULL,
  facet = feature_id,
  fixed = list(na.rm = TRUE)
)

Arguments

object

SummarizedExperiment

x

svar mapped to x

fill

svar mapped to fill

color

svar mapped to color

group

svar mapped to group

facet

svar mapped to facets

highlight

fvar expressing which feature should be highlighted

fixed

fixed aesthetics

subgroup

subgroup svar

Value

ggplot object

See Also

plot_sample_densities, plot_sample_boxplots

Examples

# data
    require(magrittr)
    file <- download_data('halama18.metabolon.xlsx')
    object <- read_metabolon(file, plot = FALSE)
    object %<>% extract(, order(.$Group))
    control_features <- c('biotin','phosphate')
    fdata(object) %<>% cbind(control=.$feature_name %in% control_features)
# plot
    plot_violins(object[1:12, ], x=feature_id, fill=feature_id)
    plot_feature_violins(object[1:12, ])
    plot_sample_violins(object[, 1:12],  highlight = control)
    plot_subgroup_violins(object[1:4, ], subgroup = Group)

[Package autonomics version 1.2.0 Index]