plot,biosign-method {biosigner} | R Documentation |
Displays classifier tiers or individual boxplots from selected features
## S4 method for signature 'biosign' plot(x, y, tierMaxC = "S", typeC = c("tier", "boxplot")[1], file.pdfC = NULL, .sinkC = NULL, ...)
x |
An S4 object of class |
y |
Currently not used. |
tierMaxC |
Character: Maximum level of tiers to display: Either 'S' and 'A', (for boxplot), or also 'B', 'C', 'D', and 'E' (for tiers) by decreasing number of selections |
typeC |
Character: Plot type; either 'tier' [default] displaying the comparison of signatures up to the selected 'tierMaxC' or 'boxplot' showing the individual boxplots of the features selected by all the classifiers |
file.pdfC |
Character: Figure filename ending with '.pdf'; default is NULL (no saving; displaying instead) |
.sinkC |
Character: Name of the file for R output diversion [default = NULL: no diversion]; Diversion of messages is required for the integration into Galaxy |
... |
Currently not used. |
A plot is created on the current graphics device.
Philippe Rinaudo and Etienne Thevenot (CEA)
## loading the diaplasma dataset data(diaplasma) attach(diaplasma) ## restricting to a smaller dataset for this example featureSelVl <- variableMetadata[, "mzmed"] >= 490 & variableMetadata[, "mzmed"] < 500 dataMatrix <- dataMatrix[, featureSelVl] variableMetadata <- variableMetadata[featureSelVl, ] ## signature selection for all 3 classifiers ## a bootI = 5 number of bootstraps is used for this example ## we recommend to keep the default bootI = 50 value for your analyzes set.seed(123) diaSign <- biosign(dataMatrix, sampleMetadata[, "type"], bootI = 5) ## individual boxplot of the selected signatures plot(diaSign, typeC = "boxplot") detach(diaplasma)