prepare_data_for_plot: Prepare data for plotting

In markrobinsonuzh/iCOBRA: Comparison and Visualization of Ranking and Assignment Methods

Prepare data for plotting

Description

Prepare performance data provided in a COBRAPerformance object (obtained by calculate_performance) for plotting.

Usage

prepare_data_for_plot(
  cobraperf,
  keepmethods = NULL,
  incloverall = TRUE,
  colorscheme = "hue_pal",
  facetted = TRUE,
  incltruth = TRUE,
  conditionalfill = TRUE
)

Arguments

cobraperf	A COBRAPerformance object.
keepmethods	A character vector consisting of methods to retain for plotting (these should be a subset of basemethods(cobraperf)), or NULL (indicating that all methods represented in cobraperf should be retained).
incloverall	A logical indicating whether the "overall" results should be included if the results are stratified by an annotation.
colorscheme	Either a character string giving the color palette to use to define colors for the different methods, or a character vector with colors to use. The available pre-defined palettes depend on the number of different methods to distinguish. The choices are: - Accent (max 8 methods) - Dark2 (max 8 methods) - Paired (max 12 methods) - Pastel1 (max 9 methods) - Pastel2 (max 8 methods) - Set1 (max 9 methods) - Set2 (max 8 methods) - Set3 (max 12 methods) - hue_pal - rainbow - heat - terrain - topo - cm If the number of allowed methods is exceeded, the colorscheme defaults to hue_pal.
facetted	A logical indicating whether the results should be split into subpanels when stratified by an annotation (TRUE), or kept in the same panel but shown with different colors (FALSE).
incltruth	A logical indicating whether the truth should be included in Venn diagrams.
conditionalfill	A logical indicating whether the points (in FDR/TPR, FDR/NBR, FSR/NBR plots) should be filled conditional on whether they satisfy the imposed criterion (e.g., false discovery rate control at imposed threshold).

Value

A COBRAPlot object

Author(s)

Charlotte Soneson

Examples

data(cobradata_example)
cobraperf <- calculate_performance(cobradata_example,
                                   binary_truth = "status",
                                   cont_truth = "none",
                                   aspects = c("fdrtpr", "fdrtprcurve",
                                               "tpr", "roc"),
                                   thrs = c(0.01, 0.05, 0.1), splv = "none")
cobraplot <- prepare_data_for_plot(cobraperf, keepmethods = NULL,
                                   colorscheme = "Dark2")

## User-specified colors
cobraplot2 <- prepare_data_for_plot(cobraperf, keepmethods = NULL,
                                   colorscheme = c("blue", "red", "green"))

markrobinsonuzh/iCOBRA documentation built on March 28, 2024, 2:01 p.m.