COBRAPlot: 'COBRAPlot' object and constructor

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

COBRAPlot object and constructor

Description

The COBRAPlot class is similar to the COBRAPerformance class in that it holds various types of calculated performance measures. However, it also contains other attributes that are necessary for plotting, such as color assignments. Several COBRAPlot objects can be generated from the same COBRAPerformance object, without having to go through the potentially time consuming task of recalculating all performance measures. Objects from this class are typically generated from a COBRAPerformance objects by means of the function prepare_data_for_plot.

Usage

COBRAPlot(
  fdrtpr = data.frame(),
  fdrtprcurve = data.frame(),
  fsrnbr = data.frame(),
  fsrnbrcurve = data.frame(),
  fdrnbr = data.frame(),
  corr = data.frame(),
  fdrnbrcurve = data.frame(),
  tpr = data.frame(),
  fpr = data.frame(),
  roc = data.frame(),
  scatter = data.frame(),
  onlyshared = NA,
  fpc = data.frame(),
  overlap = data.frame(),
  plotcolors = "",
  splv = "",
  deviation = data.frame(),
  maxsplit = NA_integer_,
  facetted = NA
)

Arguments

fdrtpr	A data frame containing observed FDR and TPR values at various adjusted p-value thresholds.
fdrtprcurve	A data frame containing observed FDR and TPR values for a (potentially large) number of cutoffs applied to a 'score' (that can be p-value, adjusted p-value or a more general score).
fsrnbr	A data frame containing observed false sign rate (FSR) and the number of features considered to be significant at various s-value thresholds
fsrnbrcurve	A data frame containing observed false sign rate (FSR) and number of features considered to be significant for a (potentially large) number of cutoffs applied to the s-value
fdrnbr	A data frame containing observed FDR and the number of features considered to be significant at various adjusted p-value thresholds.
corr	A data frame containing observed (Pearson and Spearman) correlation values between observed and true scores.
fdrnbrcurve	A data frame containing observed FDR and number of features considered to be significant for a (potentially large) number of cutoffs applied to a 'score' (that can be p-value, adjusted p-value or a more general score).
tpr	A data frame containing observed TPR values at various adjusted p-value thresholds.
fpr	A data frame containing observed FPR values at various adjusted p-value thresholds.
roc	A data frame containing observed FPR and TPR values for a (potentially large) number of cutoffs applied to a 'score' (that can be p-value, adjusted p-value or a more general score), which can be used to generate a ROC curve.
scatter	A data frame containing observed 'scores' (p-values, adjusted p-values or more general scores) and true scores, which can be used to generate scatter plots.
onlyshared	A logical value indicating whether only features shared between the results and the truth should be retained, or if all features present in the truth should be used.
fpc	A data frame containing observed numbers of false positive findings among the N top-ranked features (ranked by p-values, adjusted p-values or more general scores), for a (potentially large) number of Ns, which can be used to generate a false positive curve.
overlap	A data frame or list of data frames with binary values indicating, for each of a number of methods and number of features, whether the method consider the feature 'positive' (significant, 1) or 'negative' (non-significant, 0). If it is a list of data frames, each list element corresponds to one level of a stratifying factor.
plotcolors	A character vector giving the color for each method (or method-stratification level combination).
splv	A character string giving the name of the stratification factor, "none" if the results are not stratified.
deviation	A data frame containing deviations between observed scores and true scores.
maxsplit	A numeric value indicating the largest number of levels to retain if the results have been stratified by an annotation.
facetted	A logical indicating whether the data is prepared for a facetted plot (separating different stratification levels into different panels) or for displaying all values in one plot panel.

Value

A COBRAPlot object.

Author(s)

Charlotte Soneson

Examples

## Empty COBRAPlot object
cobraplot <- COBRAPlot()

markrobinsonuzh/iCOBRA documentation built on Nov. 7, 2024, 7:11 a.m.