compareBoxplots {TBSignatureProfiler} | R Documentation |
Present the results of AUC bootstrapping for a collection of scored signatures via boxplots.
compareBoxplots( SE_scored, annotationColName, signatureColNames, num.boot = 100, name = "Boxplot Comparison of Signature AUCs", pb.show = TRUE, abline.col = "red", fill.col = "gray79", outline.col = "black", rotateLabels = FALSE, violinPlot = FALSE )
SE_scored |
a |
annotationColName |
a character string giving the column name in
|
signatureColNames |
a vector of column names in the
|
num.boot |
an integer indicating the number of times to bootstrap the data. |
name |
a character string giving the overall title for the plot.
The default is |
pb.show |
logical for whether to show a progress bar while running code.
Default is |
abline.col |
the color to be used for the dotted line at AUC = 0.5
(the chance line). The default is |
fill.col |
the color to be used to fill the boxplots.
The default is |
outline.col |
the color to be used for the boxplot outlines.
The default is |
rotateLabels |
If |
violinPlot |
logical. Setting |
A plot with side-by-side boxplots of bootstrapped AUC values for each specified signature.
# Run signature profiling choose_sigs <- TBsignatures[c(1, 2)] prof_indian <- runTBsigProfiler(TB_indian[seq_len(25), ], useAssay = "logcounts", algorithm = "ssGSEA", signatures = choose_sigs, parallel.sz = 1) # Create boxplots compareBoxplots(prof_indian, annotationColName = "label", signatureColNames = names(choose_sigs), rotateLabels = TRUE)