characterORexpressionOrCall-class | S4 Class Union with character/expression/call |
esetLda | plot a biplot of a linear discriminant analysis of an eSet object |
esetPlot | An S4 class to represent 'esetPlot' object expressionSet with visualization data from dimension-reduction methods |
esetPlot-class | An S4 class to represent 'esetPlot' object expressionSet with visualization data from dimension-reduction methods |
esetPlotInteractive | a S4 class to represent interactive plots |
esetPlotInteractive-class | a S4 class to represent interactive plots |
esetPlotWrapper | wrapper for biplot of features/samples contained in a eSet object |
esetSpectralMap | plot a spectral map biplot of an eSet. |
esetTsne | plot a t-SNE of an eSet object |
formatManualScale | extend manual scale values if required |
formatOutput | format output of plotEset function |
getAxesLimits | generic for get axes limits |
getAxesLimits-method | generic for get axes limits |
getCoordGeneSets | extract coordinates gene sets |
getDataPlotSamplesWithAnnotation | get sample data for plot |
getDataPlotSamplesWithAnnotation-method | get sample data for plot |
getGeneSetsForPlot | get gene sets for plot of eSet object. |
getMethodsInputObjectEsetVis | wrapper to extract useful functions, depending if the object is an ExpressionSet or a SummarizedExperiment. |
ggPlotEset | visualize and esetPlot with the 'ggplot2' package |
ggplotEsetPlot | a S4 class to represent 'ggplot' plots |
ggplotEsetPlot-class | a S4 class to represent 'ggplot' plots |
ggvisEsetPlot | a S4 class for 'ggvis' plot |
ggvisEsetPlot-class | a S4 class for 'ggvis' plot |
ggvisPlotEset | visualize and esetPlot with the the 'ggvis' package |
initialize-method | An S4 class to represent 'esetPlot' object expressionSet with visualization data from dimension-reduction methods |
plotEset | plot an plotEset object |
plotEset-method | plot an plotEset object |
plotTopElements | create 'geom_text' object with top genes/sample/pathways |
rbokehEsetPlot | a S4 class to represent 'rbokeh' plots |
rbokehEsetPlot-class | a S4 class to represent 'rbokeh' plots |
rbokehPlotEset | visualize and esetPlot with the the 'rbokeh' package |
setFixElement | check if the aesthetic is fixed (e.g. color, shape, size 'palette') |
setManualScale | check if manual aesthetic should be set |
simpleCap | capitalize the first letter of a word |