Prepare data for plotting

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

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")
#> Warning: Object doesn't have a slot sval. Please run update_cobradata(). For consistency, I will return an empty data.frame
#> column DESeq2 is being ignored for NBRS calculations
#> column DESeq2 is being ignored for TPR calculations
#> column DESeq2 is being ignored for FDR calculations
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"))