prepare_data_for_plot {iCOBRA} | R Documentation

## 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"))

[Package iCOBRA version 1.15.1 Index]