# Shiny apps for NGS data

## Documentation for package ‘shinyngs’ version 1.8.2

- DESCRIPTION file.

## Help Pages

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
anova_pca_metadata | Generate a matrix of anova values for associating principal components with categorical covariates.
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 (>, < ..).
checkListIsSubset | Check one list is a subset of another and throw an error if not
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
cond_log2_transform_assays | Conditionally apply log2 transformation on assay data based on log2_assays parameter.
cond_log2_transform_matrix | Apply log2 transformation on a matrix.
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
getExtension | Extract the extension of a file
getSeparator | Infer a separator from the extension of an input file
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
is_valid_positive_integer_vector | Check if a comma-separated string can be parsed to an integer vector

## -- 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_contrasts | Read and validate a contrasts file against sample metadata
read_differential | Read tables of differential statistics
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 --

validate_indices | Validate assay indices based on a given string.
validate_inputs | Call the various read/ validate methods for input data surrounding an experiment
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