Interactive Highcharts Boxplot for Proteomics

Usage

boxplot_highchart_list(
  data,
  assays = NULL,
  color_by = "Condition",
  group_order = NULL,
  palette = NULL,
  title = NULL,
  subtitle = NULL,
  show_outliers = TRUE,
  outlier_jitter = 0.15,
  outlier_size = 3,
  box_width = 20,
  horizontal = TRUE,
  height = NULL
)

Arguments

data: Data frame with columns: Column, Assay, Intensity, Condition
assays: Vector of assays to include (NULL = all of them)
color_by: Column used for colouring (default: "Condition")
group_order: Order of the groups/conditions
palette: Colour palette: "ggsci::palette", "brewer:Name", or a vector
title: Chart title (optional). Use {assay} as a placeholder (e.g. "Boxplot: {assay}" -> "Boxplot: ImpSeqRob_Min")
subtitle: Chart subtitle (optional). Use {assay} as a placeholder
show_outliers: Show outliers lying outside the whiskers (default: TRUE)
outlier_jitter: Amount of horizontal jitter applied to the outliers (default: 0.15)
outlier_size: Radius of the outlier points (default: 3)
box_width: Width of the boxplot boxes in pixels (default: 20)
horizontal: Horizontal orientation (default: TRUE)
height: Chart height in pixels

Value

List of highchart objects (one per assay)

Examples

data(nadia_dia)
res <- process_proteomics(nadia_dia, verbose = FALSE)

# One boxplot per assay; keep only the imputed one
hc_list <- boxplot_highchart_list(
  res$BoxPlot_Input,
  assays      = "Impseqrob_min",
  group_order = c("A", "B", "D"),
  title       = "Boxplot: {assay}"
)
names(hc_list)
#> [1] "Impseqrob_min"