Shiny apps for NGS data


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Documentation for package ‘shinyngs’ version 1.7.2

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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
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
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 --

ensureLog Ensure a matrix is in log scale
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

-- 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_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