Man pages for cusom/CUSOM.ShinyHelpers
CU School of Medicine Helper Functions for Shiny Applications
| addGroupCount | Adds HTML formatted count to group variable |
| addSignificanceGroup | Function to add 3 group significance group label to fold... |
| applyGroupCountThreshold | Utility function to check for minimum group membership in a... |
| calculateFoldChangeByKeyGroup | Calculate fold change for each key value between groups |
| createApplicationLinks | Utility function to create application link buttons |
| createFieldSet | Create tag list of field sets |
| createInputControl | Utility function to create standard Shiny input widgets |
| createMenuItem | Creates Shiny Dashboard Menu Item / Tab |
| createServerObject | utility function to import shiny modules to server |
| createSidebarInputs | Utility function to create Shiny UI inputs within the sidebar... |
| createTabOutput | Utility function to create Tab Items |
| createTooltip | returns standard text with info-circle tooltip. If... |
| createTutorialTooltip | returns standard turtorial text with info-circle tooltip. If... |
| dbConnector | Function to create DBI odbc database connection object |
| depth | Check depth of a list |
| dfrapply | Recursively apply function to all data.frames in a nested... |
| dfToTree | Converts a data.frame to a data.tree format |
| downloadFile | Utility module to assist in dataset downloads |
| fillMissingSexObservations | Utility function to fill in missing missing conbinations... |
| formatFoldChangeDataframe | Apply standard formatting to fold change dataframe |
| formatPValue | formats significance Variable value value based on threshold... |
| getBoxplot | Plotly function to generate standard box and whisker plot |
| getBoxplotForEmptyData | Utility Plotly function to return blank plot when useful |
| getBoxPlotWithHighlightGroup | Plotly function to generate standard box and whisker plot... |
| getBoxPlotWithSelectedRecords | Plotly function to generate standard box and whisker plot... |
| getCorrelationsByKey | Calculate correlations between key var and all other keys in... |
| getCorrelationVolcanoAnnotations | gets all possible correlation volcano plot annotations in a... |
| getDataframeFromDatabase | Function to pull data from database using paramterized DBI... |
| getDefaultVolcanoAnnotations | volcano plot Plotly function to get standard volcano... |
| getDefaultVolcanoLine | volcano plot Plotly function to get standard volcano line... |
| getDensityColors | Wrapper function around grDevices::densCols produces a vector... |
| getExternalLinkActionLinks | Utility function to create standard external site links for a... |
| getExternalLinkTooltip | Utility function to create tooltip for external links for a... |
| getGroupedBoxplot | Plotly function to generate multiple box and whisker plots... |
| getGroupedStatAnnotations | function to generate stat annotations across multiple groups |
| getGroupedStatTestByKeyGroup | function to run stat tests for multiple groups |
| getLinearModel | run linear model |
| getLinearModelWithInteraction | run linear model with interaction between independent... |
| getMaxAbsValue | gets maximum abs value from dataframe column |
| getRadioButton | get a pretty radio button with HTML tooltip choice names,... |
| getScatterPlotByGroup | generate scatter plot colored by group optionally add linear... |
| getScatterPlotWithSmoothing | GGplot function to generate standard volcano plot from fold... |
| getSelectedRecordsAgePlot | get Plotly box and whisker plot showing age distribution by... |
| getSelectedRecordsSexPlot | get Plotly stacked bar chart showing distribution by sex for... |
| getSideBySideGroupedBoxplot | Plotly function to generate side-by-side box and whisker... |
| getSOMStandardFooter | Utility function to get standard School of Medicine Footer... |
| getStatAnnotationAnchorLines | function to generate list of line anchors for stat... |
| getStatTestByKeyGroup | Calculate statistical test between 2 groups for each key... |
| getStatTestByKeyGroup.adjustment.methods | Return available adjustmemt methodss |
| getStatTestByKeyGroup.methods | Return implemented stat test methods |
| getVolcanoAnnotations | gets all possible volcano plot annotations in a single call.... |
| getVolcanoArrowAnnotation | volcano plot Plotly function to add volcano plot arrow... |
| getVolcanoPlot | Plotly function to generate standard volcano plot from fold... |
| nodesToDf | Convert the nodes of a tree into a data.frame |
| parseDelimitedString | parses a delimited string looking for standard set of... |
| plotGSEAEnrichment | Generate a plotly-based GSEA Enrichment plot |
| prettyRadioButtonsFieldSet | Create a group of radio buttons with common input |
| runfGSEA | Run 2-sided fgseaMultilevel analysis (positive and negative)... |
| stackList | Combine named list into single data.frame with extra column |
| summarizeByGroup | Calculate standard summaries across groups for a dataframe |
| treeToDf | Convert tree into data.frame |
| treeToJSON | Converts a data.tree to a JSON format |
