Shiny apps for NGS data
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Documentation for package ‘shinyngs’ version 1.3.0
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A B C D E F G H I L M N P R S U V misc
-- A --
| addPoints | Add points to a plotly object |
| addTextLabels | Add permanent text labels to points in a plotly graph |
| adjustLayout | Apply layout adjustments to plotly object |
| annotatedHeatmap | Make a heatmap with annotations by experimental variable |
| assaydatatable | The server function of the assaydatatable module |
| assaydatatableInput | The UI input function of the assaydatatable module |
| assaydatatableOutput | The output function of the assaydatatable module |
-- B --
| barcode_plot | Make a gene set barcode plot using Limma |
| barplot | Server function of the 'barplot' module |
| barplotInput | Input function of the 'barplot' module |
| barplotOutput | Output function of the 'barplot' module |
| bootstrapMedian | Bootstrap the standard error of the median |
| boxplot | The server function of the boxplot module |
| boxplotInput | The input function of the boxplot module |
| boxplotOutput | The output function of the boxplot module |
-- C --
| calculateDendrogram | Calculate a clustering dendgrogram based on correlation |
| calculateDist | Calculate a distance matrix based on correlation |
| calculatePCAFractionExplained | Extract the percent variance from a PCA analysis |
| cardinalNumericField | Make a numeric field with selectable associated cardinality (>, < ..). |
| chipseq | The server function of the chipseq module. Currently a near-clone of the RNA-seq module, with ChIP-seq optimisations planned. |
| chipseqInput | The input function of the chipseq module. Currently a near-clone of the RNA-seq module, with ChIP-seq optimisations planned. |
| chooseGroupingVariables | Choose a valid set of grouping variables from a targets/ experiment data frame. |
| clustering | The server function of the clustering module |
| clusteringDendrogram | Make a clustering dendrogram with coloring by experimental variable |
| clusteringInput | The input function of the clustering module |
| clusteringOutput | The output function of the clustering module |
| colGeomMeans | Geometric means by matrix column |
| colMedians | Medians by matrix column |
| colormaker | The output function of the colorby module |
| colormakerInput | The input function of the colorby module |
| compilePCAData | Run PCA on a given matrix, expected to be variance stabilised (at least log-transformed) |
| compile_contrast_data | Compile contrast stats for inclusion in shinyngs |
| contrasts | The server function of the contrasts module |
| contrastsInput | The input function of the contrasts module |
| contrastsOutput | The output function of the contrasts module |
| convertIds | Convert row names to metadata identifiers |
-- D --
| dendro | The server function of the dendrogram module |
| dendroInput | The input function of the dendrogram module |
| dendroOutput | The output function of the dendro module |
| dexseqplot | The server function of the dexseqplot Shiny module |
| dexseqplotInput | The UI input function of the dexseqplot Shiny module |
| dexseqplotOutput | The UI output function of the dexseqplot Shiny module. Produces a plot and a table of values. |
| dexseqtable | The server function of the dexseqtable module |
| dexseqtableInput | The UI input function of the dexseqtable module |
| dexseqtableInputFields | Make input fields for producing a table of differential exon usage. Separated here for re-use by the dexseqplot module |
| dexseqtableOutput | The output function of the dexseqtable module |
| differentialtable | The server function of the differentialtable module |
| differentialtableInput | The UI input function of the differentialtable module |
| differentialtableOutput | The output function of the differentialtable module |
| drawLines | Overlay lines on a plotly-generated plot |
-- E --
| eselistfromConfig | Build an ExploratorySummarisedExperimentList from a description provided in a list |
| eselistFromYAML | Build an ExploratorySummarisedExperimentList from a YAML description |
| evaluateCardinalFilter | Evaluate a vector of values with respect to a limit and a cardinality, being '>', '<' , '> or <-' (e.g. a fold change above a limit in + or - directions), or '< and >-' (not a above a limit in + or -). |
| experimenttable | The server function of the experimenttable module |
| experimenttableInput | The UI input function of the experimenttable module |
| experimenttableOutput | The output function of the experimenttable module |
| ExploratorySummarizedExperiment | ExploratorySummarizedExperiments |
| ExploratorySummarizedExperiment-class | The ExploratorySummarizedExperiment class |
| ExploratorySummarizedExperimentList | ExploratorySummarizedExperimentLists, containers for ExploratorySummarizedExperiments |
| ExploratorySummarizedExperimentList-class | The ExploratorySummaizedExperimentList class |
-- F --
| fieldSets | Create sets of fields for display |
| foldChange | Calculate fold change between two vectors |
| foldchangeplot | The server function of the 'foldchangeplot' module |
| foldchangeplotInput | The UI input function of the 'foldchangeplot' module |
| foldchangeplotOutput | The output function of the 'foldchangeplot' module |
-- G --
| gene | The server function of the gene module |
| geneBarplot | Main function for drawing the bar plot with plotly |
| geneInput | The input function of the gene module |
| geneModelPlot | Make a gene model plot for a chromosomal location |
| geneOutput | The input function of the gene module |
| geneselect | The server function of the geneselect module |
| geneselectInput | The UI input function of the geneselect module |
| genesetanalysistable | The server function of the genesetanalysistable module |
| genesetanalysistableInput | The UI input function of the genesetanalysistable module |
| genesetanalysistableOutput | The output function of the genesetanalysistable module |
| genesetbarcodeplot | The server function of the genesetbarcodeplot module |
| genesetbarcodeplotInput | The UI input function of the genesetbarcodeplot module |
| genesetbarcodeplotOutput | The output function of the genesetbarcodeplot module |
| genesetselect | The server function of the genesetselect module |
| genesetselectInput | The UI function of the genesetselect module |
| geom_mean | Geometric mean |
| ggplotify | Reshape data to the way 'ggplot2' likes it |
| ggplot_boxplot | Make a boxplot with coloring by experimental variable |
| ggplot_densityplot | Make a static density plot with ggplot2 |
| groupby | The server function of the groupby module |
| groupbyInput | The UI function of the groupby module |
-- H --
| heatmap | The server function of the heatmap module |
| heatmapInput | The input function of the heatmap module |
| heatmapOutput | The output function of the heatmap module |
| hiddenInput | Make a hidden input field. Handy for replacing superfluous single-value selects etc |
-- I --
| idToLabel | Create row labels based on the settings of 'labelfield' in the 'ExploratorySummarizedExperiment' object and the annotation data in 'mcols'. |
| illuminaarray | The server function of the illuminaarray module |
| illuminaarrayInput | The input function of the illuminaarray module |
| illuminaarrayqc | The server function of the illuminaarrayqc module |
| illuminaarrayqcInput | The input function of the illuminaarrayqc module |
| illuminaarrayqcOutput | The output function of the illuminaarrayqc module |
| inlineField | Wrap a Shiny input so its label is displayed inline |
| interactiveHeatmap | Make a ineractive heatmap with d3heatmap |
| interleaveColumns | Interleave the columns of two matrices of equal dimensions |
-- L --
| labelMatrix | Add columns to display ID and label in a table |
| labelselectfield | The server function of the 'labelselectfield' module |
| labelselectfieldInput | The input function of the 'labelselectfield' module |
| linkMatrix | Add links to a table |
-- M --
| madScore | Calculate MAD scores as per OmicSoft |
| makeAnnotationColors | Make color sets to use in heatmap annotation |
| makeColorScale | Make a color palette of a specified length |
| makeContrastControl | Make a select field for picking one or more contrasts |
| makeContrastFilterSet | Make a complete set of filters for a contrast: the contrast itself, fold change, and where applicable p- and q- values. |
| makePackageCitation | Return a usable citation string for a package |
| maplot | The server function of the 'maplot' module |
| maplotInput | The UI input function of the 'maplot' module |
| maplotOutput | The output function of the 'maplot' module |
| modalInput | The input function for the 'modal' module |
| modalOutput | The output function of the 'modal' module |
-- N --
| na.replace | Replace NAs with a string for convenience |
| nlines | Count the number of lines in a string |
-- P --
| pca | The server function of the pca module |
| pcaInput | The input function of the pca module |
| pcaOutput | The output function of the pca module |
| plotdownload | The server function of the gene set module |
| plotdownloadInput | The input function of the gene plotdownload module |
| plotly_boxplot | Make a boxplot with coloring by experimental variable |
| plotly_densityplot | Make a dynamic density plot with plotly |
| plotly_quartiles | Make a line-based alternative to boxplots |
| plotly_scatterplot | Make scatterplots with 'plot_ly()' |
| prepareApp | Make UI and server functions for Shiny apps based on data supplied as modfied SummarizedExperiments |
| prettifyGeneSetName | Prettify gene set names like those from MSigDB |
| prettifyVariablename | Make machine variable names pretty for display |
| pushToList | Simple list push |
-- R --
| readreports | Server function of the 'readreports' module |
| readreportsInput | Input function of the 'readreports' module |
| readreportsOutput | Output function of the 'readreports' module |
| read_matrix | Read an expression matrix file and match to specified samples and features |
| read_metadata | Read a metadata file |
| rnaseq | The server function of the rnaseq module |
| rnaseqInput | The input function of the rnaseq module |
| rowmetatable | The server function of the rowmetatable module |
| rowmetatableInput | The UI input function of the rowmetatable module |
| rowmetatableOutput | The output function of the rowmetatable module |
| runPCA | Run a simple PCA analysis |
-- S --
| sampleselect | The server function of the sampleselect module |
| sampleselectInput | The UI input function of the sampleselect module |
| scatterplot | Server function for the scatterplot module |
| scatterplotcontrols | Server function for scatterplotcontrols module |
| scatterplotcontrolsInput | Input function for scatterplotcontrols module |
| scatterplotInput | Input function for the scatterplot module |
| scatterplotOutput | Output function for the scatterplot module |
| selectmatrix | The server function of the selectmatrix module |
| selectmatrixInput | The UI input function of the selectmarix module |
| selectVariableGenes | Generate an integer ordering to select the n most variable genes out of a matrix |
| shinyngs | Interactive downstream analysis with ShinyNGS. |
| simpleApp | Produce a simple app with controls and layout for a single module, in a shiny 'sideBarLayout()'. |
| simpleSplit | Convenience interface to strsplit() |
| simpletable | The server function of the simpletable module |
| simpletableInput | The UI input function of the simpletable module |
| simpletableOutput | The output function of the simpletable module |
| simplifyContrastTable | Simplify a contrast table |
| singleValidMatrix | Is there only one matrix to plot from this object? |
| splitStringToFixedwidthLines | Given a string with spaces, try to split into multiple lines of < 'linewidth' characters |
| static_scatterplot | Make scatterplots with 'ggplot()' or 'scatterplot3d' |
| stringsToNamedVector | Take two delimiter-separated strings and generate a named vector |
| summarisematrix | The server function of the summarisematrix module |
| summarisematrixInput | The input function of the summarizematrix module |
| summarizeMatrix | Summarise the rows of a matrix, applying a function to groups of cells defined by a factor |
| summarySE | Summarise an input matrix |
-- U --
| ucfirst | Capitalise the first letter of a string |
| unpack.list | Unpack a list to the environment. Handy when many reactive functions are returned by a call to a module's server function |
| upset | The server function of the upstart module |
| upsetInput | The input function of the upset module |
| upsetOutput | The output function of the clustering module |
-- V --
| volcanoplot | The server function of the 'volcanoplot' module |
| volcanoplotInput | The UI input function of the 'volcanoplot' module |
| volcanoplotOutput | The output function of the 'volcanoplot' module |
-- misc --
| [-method | The ExploratorySummaizedExperimentList class |