dataPlot {KnowSeq} | R Documentation |
This function allows to plot different charts only by changing the parameters, for the different KnowSeq pipeline steps. Furthermore, the chosen plot can be saved to PNG and PDF.
dataPlot(data, labels, colours = c("green", "red"), main = "", ylab = "Expression", xlab = "Samples", legend = "", mode = "boxplot", clusters = 2, toPNG = FALSE, toPDF = FALSE)
data |
Normally, the data parameter is an expression matrix or data.frame, however for the confusionMatrix plot, the data are a confussion matrix that can be achieved by using the output of any of the machine learning functions of this package. |
labels |
A vector or factor that contains the labels for each of the samples in the data parameter. |
colours |
A vector that contains the desired colours to plot the different charts. Example: c("red","green","blue"). |
main |
The title for the plot. |
ylab |
The description for the y axis. |
xlab |
The description for the x axis. |
legend |
A vector with the elements in the legend of the plot. |
mode |
The different plots supported by this package. The possibilities are boxplot, orderedBoxplot, genesBoxplot, heatmap, optimalClusters, knnClustering, confusionMatrix and classResults. |
clusters |
The number of optimal clusters for the data parameter calculated with this function in mode optimalCluster. This is useful to know the possible clusters formed due to the batch effect. |
toPNG |
Boolean variable to indicate if a plot would be save to PNG. |
toPDF |
Boolean variable to indicate if a plot would be save to PDF. |
Nothing to return.
dir <- system.file("extdata", package="KnowSeq") load(paste(dir,"/expressionExample.RData",sep = "")) dataPlot(expressionMatrix,labels,mode = "boxplot",toPNG = TRUE,toPDF = TRUE) dataPlot(DEGsMatrix[1:12,],labels,mode = "orderedBoxplot",toPNG = TRUE,toPDF = TRUE) dataPlot(DEGsMatrix[1:12,],labels,mode = "genesBoxplot",toPNG = TRUE,toPDF = FALSE) dataPlot(DEGsMatrix[1:12,],labels,mode = "heatmap",toPNG = TRUE,toPDF = TRUE)