htShinyExample.RdExamples of interactive complex heatmaps
htShinyExample(which)
| which | An index of which example to use. The list of all examples can be obtained by executing |
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In every example, there is a Shiny app opened, which also includes source code that generates this app.
A Shiny app object.
# list all examples htShinyExample()#> There are following examples. Individual example can be run by e.g. htShinyExample(1.1). #> #> ──────── 1. Simple examples ───────────────────────────────────────────────────────── #> 1.1 A single heatmap with minimal arguments. #> 1.2 A single heatmap from a character matrix. #> 1.3 A single heatmap with annotations on both rows and columns. #> 1.4 A single heatmap where rows and columns are split. #> 1.5 A list of two heatmaps. #> 1.6 A list of two vertically concatenated heatmaps #> 1.7 Use last generated heatmap, an example from cola package. #> 1.8 Use last generated heatmap, an app with three interactive heatmaps #> 1.9 Demonstrate hover, click and dblclick actions to select cells. #> 1.10 Only response to one of click/hover/dblclick/hover events. Please use #> htShinyExample('1.10') to get this example (quote the index, or else #> htShinyExample(1.10) will be treated as the same as htShinyExample(1.1)). #> 1.11 Interactive heatmap under compact mode. #> #> ──────── 2. On other plots and packages ───────────────────────────────────────────── #> 2.1 A density heatmap. #> 2.2 An oncoPrint. #> 2.3 A UpSet plot. #> 2.4 An interactive heatmap from pheatmap(). #> 2.5 An interactive heatmap from heatmap(). #> 2.6 An interactive heatmap from heatmap.2(). #> 2.7 A heatmap produced from tidyHeatmap package. #> 2.8 Genome-scale heatmap. #> 2.9 A package-dependency heatmap. You can try to control "Fill figure region" #> and "Remove empty rows and columns" in the tools under the sub-heatmap. #> #> ──────── 3. Enriched heatmaps ─────────────────────────────────────────────────────── #> 3.1 A single enriched heatmap. #> 3.2 A list of enriched heatmaps. #> 3.3 An enriched heatmap with discrete signals. #> #> ──────── 4. On public datasets ────────────────────────────────────────────────────── #> 4.1 An example from Lewis et al 2019. #> 4.2 Visualize cell heterogeneity from single cell RNASeq. #> 4.3 Correlations between methylation, expression and other genomic features. #> #> ──────── 5. Shiny app development ─────────────────────────────────────────────────── #> 5.1 A single Shiny app with two interactive heatmap widgets. #> 5.2 Self-define the output. The selected sub-matrix is shown as a text table. #> 5.3 Self-define the output. Additional annotations for the selected genes are #> shown. #> 5.4 Visualize Gene Ontology similarities. A list of selected GO IDs as well as #> their descriptions are shown in the output. #> 5.5 Interactive correlation heatmap. Clicking on the cell generates a #> scatterplot of the two corresponding variables. #> 5.6 A heatmap on Jaccard coefficients for a list of genomic regions. Clicking #> on the cell generates a Hilbert curve of how the two sets of genomic #> regions overlap. #> 5.7 Implement interactivity from scratch. Instead of generating the whole #> interactive heatmap widget, it only returns the information of rows and #> columns that user have selected on heatmap and users can use this #> information to build their own interactive heatmap widgets. #> 5.8 Implement interactivity from scratch. A visualization of 2D density #> distribution. Brushing on heatmap triggers a new 2D density estimation #> only on the subset of data. #> #> ──────── 6. Dynamically generate heatmap widget in Shiny app ──────────────────────── #> 6.1 The matrix with different dimensions is dynamically generated. #> 6.2 Reorder by a column that is specified by user. #> 6.3 Dynamically generate the widget with InteractiveComplexHeatmapModal(). The #> modal is triggered by an action button. #> 6.4 Dynamically select interactive heatmaps. The modal is triggered by radio #> buttons. #> 6.5 Dynamically generate the widget. A customized Javascript code is inserted #> after the UI to change the default behavior of the action button. #> 6.6 The widget is generated by InteractiveComplexHeatmapWidget() where the UI #> is directly put in the place defined by htmlOutput(). #> 6.7 The widget is generated by InteractiveComplexHeatmapWidget() and a #> customized Javascript code is inserted after the UI. #> #> ──────── 7. Interactive R markdown document ───────────────────────────────────────── #> 7.1 Integrate in an interactive R Markdown document. #> 7.2 Integrate in an interactive R Markdown document where the heatmap widgets #> are dynamically generated. #> #> ──────── 8. Interactivate heatmaps indirectly generated by heatmap()/heatmap.2()/pheatmap() #> 8.1 Indirect use of pheatmap(). #> 8.2 Indirect use of heatmap.2(). #> 8.3 Two interactive heatmap widgets from indirect use of pheatmap(). #> #> ──────── 9. Float output UI along with mouse positions ────────────────────────────── #> 9.1 A simple example that demonstrates output UI floating with the three #> actions: hover, click and dblclick. #> 9.2 Floating self-defined outputs. #> 9.3 Floating output only from one event on heatmap, i.e. #> hover/click/dblclick/brush-output. #> #> ──────── 10. Work with shinydashboard ──────────────────────────────────────────────── #> 10.1 Separate the three UI components into three boxes. #> 10.2 The three UI components are draggable. #> 10.3 A Shiny dashboard with two tabs. #> 10.4 Only contain the original heatmap where output floats. #> 10.5 A complex dashboard that visualizes a DESeq2 results. #>