plot_fdrtprcurve: Plot TPR vs FDR

In iCOBRA: Comparison and Visualization of Ranking and Assignment Methods

Description

Plot observed true positive rate (TPR) vs observed false discovery rate (FDR), for given adjusted p-value thresholds and/or as curves traced out by considering all threshold values.

Usage

plot_fdrtprcurve(
  cobraplot,
  title = "",
  stripsize = 15,
  titlecol = "black",
  pointsize = 5,
  xaxisrange = c(0, 1),
  yaxisrange = c(0, 1),
  plottype = c("curve", "points"),
  linewidth = 1
)

Arguments

cobraplot	A COBRAPlot object.
title	A character string giving the title of the plot.
stripsize	A numeric value giving the size of the strip text, when the results are stratified by an annotation.
titlecol	A character string giving the color of the title.
pointsize	A numeric value giving the size of the plot characters.
xaxisrange	A numeric vector with two elements, giving the lower and upper boundary of the x-axis, respectively.
yaxisrange	A numeric vector with two elements, giving the lower and upper boundary of the y-axis, respectively.
plottype	A character vector giving the type of plot to construct. Can be any combination of the two elements "curve" and "points".
linewidth	The line width used for plotting

Value

A ggplot object

Author(s)

Charlotte Soneson

Examples

data(cobradata_example)
cobraperf <- calculate_performance(cobradata_example,
                                   binary_truth = "status",
                                   aspects = c("fdrtpr", "fdrtprcurve"))
cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = "Dark2",
                                   incltruth = TRUE)
plot_fdrtprcurve(cobraplot, plottype = c("curve", "points"))

Example output

column DESeq2 is being ignored for NBRS calculations
column DESeq2 is being ignored for TPR calculations
column DESeq2 is being ignored for FDR calculations
Warning message:
Removed 3 rows containing missing values (geom_path). 

iCOBRA documentation built on April 17, 2021, 6:07 p.m.