plot_boxplots {autonomics}

R Documentation

Plot sample/feature boxplots

Description

Plot sample/feature boxplots

Usage

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

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

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

plot_subgroup_boxplots(
  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
facet	svar mapped to facet
highlight	fvar expressing which feature should be highlighted
fixed	fixed aesthetics
subgroup	subgroup svar symbol

Value

ggplot object

See Also

plot_sample_densities, plot_sample_violins

Examples

# data
    require(magrittr)
    file <- download_data('halama18.metabolon.xlsx')
    object <- read_metabolon(file, plot = FALSE)
    object %<>% extract(, order(.$Group))
    fdata(object) %<>% cbind(
                        control=.$feature_name %in% c('biotin','phosphate'))
# plot
    plot_boxplots(object[1:9,], x = feature_id, fill = feature_id)
    plot_boxplots(object[,1:9], x = sample_id,  fill = sample_id )
    plot_feature_boxplots(object[1:9, ])
    plot_sample_boxplots(object[, 1:12])
    plot_sample_boxplots(object[, 1:12], highlight = control)
    plot_subgroup_boxplots(object[1:2, ], subgroup = Group)

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