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| 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 |