benchmarkMotifsROC: Plot ROC or precision-recall curves for motifs search...

In vitkl/SLIMFinderR: Short Linear Motif Search Using QSLIMFinder, Protein Interaction Network and Binding Domain Inference

Description

Plot ROC or precision-recall curves for motifs search benchmark

Usage

benchmarkMotifsROC(res, data_type = c("both", "query", "all")[1],
  col_query = c("grey"), col_all = c("black"), ...,
  text_args = "col = \"black\"", ROCR_data = F,
  legend_args = "x = 0.8 | y = 0.25", x_query = 0.25, x_all = 0.75,
  measure1 = "tpr", measure2 = "fpr", single_metric = c("auc",
  "prbe")[1], single_metric_name = c("Median AUC",
  "Precision-recall break-even point")[1],
  summarise_single_metric = c("median", "")[1],
  both_metrics_vs_cutoff = F)

mBenchmarkMotifsROC(res_list, data_type = "query", ...)

Arguments

res	object class benchmarkMotifsResult, the output of benchmarkMotifs
...	args passed to plot
text_args	character 1L, arguments to text and legend that allow to manipulate the median AUC and legend on the plot
ROCR_data	logical, return ROC performance data? If FALSE the function only plots ROC curve
legend_args	character 1L, arguments to text and legend that allow to manipulate the median AUC and legend on the plot
measure1	character, for example "tpr" or "prec", details: ?ROCR::performance
measure2	character, for example "fpr" or "rec", details: ?ROCR::performance
res_list	list of objects of class benchmarkMotifsResult, the output of mBenchmarkMotifs
type	benchmark (test if known motifs were observed) in query proteins or in all proteins the sequences of which were used in QSLIMFinder search

Value

benchmarkMotifsROC: list of ROCR objects (prediction, performance, auc.performance) used to plot ROC curve

mBenchmarkMotifsROC: list of lists of ROCR objects (prediction, performance, auc.performance) used to plot ROC curve

Author(s)

Vitalii Kleshchevnikov

Vitalii Kleshchevnikov

See Also

benchmarkMotifs

benchmarkMotifs

vitkl/SLIMFinderR documentation built on May 3, 2019, 8:08 p.m.