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)

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