Package index • shinyngs

Building apps

Core classes and entry points for assembling an ExploratorySummarizedExperimentList and turning it into a Shiny app.

ExploratorySummarizedExperiment(): ExploratorySummarizedExperiments
ExploratorySummarizedExperimentList(): ExploratorySummarizedExperimentLists, containers for ExploratorySummarizedExperiments
prepare_app(): Make UI and server functions for Shiny apps based on data supplied as modfied SummarizedExperiments
eselist_from_yaml(): Build an ExploratorySummarisedExperimentList from a YAML description
eselist_from_config(): Build an ExploratorySummarisedExperimentList from a description provided in a list

Reading and validating input

Helpers for reading matrices, metadata, contrasts and enrichment results from files, and validating them for consistency.

read_contrasts(): Read and validate a contrasts file against sample metadata
read_differential(): Read tables of differential statistics
read_gmt(): Read a GMT-format gene set file
read_matrix(): Read an expression matrix file and match to specified samples and features
read_metadata(): Read a metadata file
file_extension(): Extract the extension of a file
guess_separator(): Infer a separator from the extension of an input file
check_list_is_subset(): Check one list is a subset of another and throw an error if not
validate_indices(): Validate assay indices based on a given string.
validate_inputs(): Call the various read/ validate methods for input data surrounding an experiment
validate_or_catch(): Evaluate an expression, converting any error into a Shiny validation message
is_valid_positive_integer_vector(): Check if a comma-separated string can be parsed to an integer vector
single_valid_matrix(): Is there only one matrix to plot from this object?
has_slot_data(): Check whether a list-type slot on an S4 object is populated
build_enrichment_path(): Build path to the enrichment results
choose_grouping_variables(): Choose a valid set of grouping variables from a targets/ experiment data frame.

Matrix and statistics utilities

Functions for transforming, summarising and clustering expression matrices.

bootstrap_median(): Bootstrap the standard error of the median
col_geom_means(): Geometric means by matrix column
col_medians(): Medians by matrix column
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.
fold_change(): Calculate fold change between two vectors
guess_foldchange_scale(): Guess whether fold change values are on a log2 or linear scale
mad_score(): Calculate MAD scores as per OmicSoft
resolve_deprecated_unlog_foldchanges(): Map the deprecated unlog_foldchanges/--unlog_foldchanges argument onto fold_change_scale, warning if it was used
resolve_foldchange_scale(): Resolve the scale of a fold-change column, cross-checking a user declaration and a column-naming convention against the observed data
run_clustering(): Partition the rows of a matrix into clusters with clara()
select_variable_genes(): Generate an integer ordering to select the n most variable genes out of a matrix
simple_split(): Convenience interface to strsplit()
summarize_matrix(): Summarise the rows of a matrix, applying a function to groups of cells defined by a factor
summary_se(): Summarise an input matrix
calculate_dist(): Calculate a distance matrix based on correlation
calculate_dendrogram(): Calculate a clustering dendrogram based on correlation
clustering_dendrogram(): Make a clustering dendrogram with coloring by experimental variable
compile_pca_data(): Run PCA on a given matrix, expected to be variance stabilised (at least log-transformed)
anova_pca_metadata(): Generate a matrix of anova values for associating principal components with categorical covariates.
interleave_columns(): Interleave the columns of two matrices of equal dimensions

Plotting functions

Standalone plotting functions reused by the Shiny modules for static and interactive output.

static_boxplot(): Make a boxplot with coloring by experimental variable
static_densityplot(): Make a static density plot with ggplot2
static_topgene_boxplots(): Make a faceted boxplot of the top differential genes in a contrast
ggplotify(): Reshape data to the way ggplot2 likes it
interactive_heatmap(): Make an interactive heatmap with heatmaply
interactive_barcodeplot(): Make an interactive gene set barcode plot with plotly
interactive_barchart(): Make a grouped, stacked or overlaid bar chart with plot_ly()
interactive_boxplot(): Make an interactive boxplot with coloring by experimental variable
interactive_cluster_profiles(): Plot expression profiles for a set of feature clusters with plot_ly()
interactive_clustering_dendrogram(): Make an interactive clustering dendrogram colored by experimental variable
interactive_count_barplot(): Plot counts of feature annotation rows by category, optionally split by a second categorical column, with plot_ly()
interactive_densityplot(): Make a dynamic density plot with plotly
interactive_illumina_control_probes(): Make an Illumina microarray control-probe QC plot with plot_ly()
interactive_pca_metadata_heatmap(): Make a PCA-vs-metadata association heatmap with heatmaply()
interactive_pca_variance_heatmap(): Combine the PCA-vs-metadata heatmap with a synced scree plot
interactive_quartiles(): Make a line-based alternative to boxplots
interactive_scatterplot(): Make scatterplots with plot_ly()
interactive_screeplot(): Make a PCA scree plot with plot_ly()
interactive_topgene_boxplots(): Make an interactive faceted boxplot of the top differential genes in a contrast
interactive_upset(): Make an UpSet-style set intersection plot with plot_ly()
static_scatterplot(): Make scatterplots with ggplot() or scatterplot3d
make_color_scale(): Make a categorical colour scale of a specified length

Identifiers, labels and gene sets

convert_ids(): Convert row names to metadata identifiers
id_to_label(): Create row labels based on the settings of labelfield in the ExploratorySummarizedExperiment object and the annotation data in mcols.
prettify_gene_set_name(): Prettify gene set names like those from MSigDB
prettify_variable_name(): Make machine variable names pretty for display
strings_to_named_vector(): Take two delimiter-separated strings and generate a named vector

Shiny UI helpers

hidden_input(): Make a hidden input field. Handy for replacing superfluous single-value selects etc
inline_field(): Wrap a Shiny input so its label is displayed inline
with_help_icon(): Append a help icon carrying a tooltip to a label

General utilities

na_replace(): Replace NAs with a string for convenience
count_lines(): Count the number of lines in a string
push_to_list(): Simple list push
split_string_to_fixed_width_lines(): Given a string with spaces, try to split into multiple lines of < linewidth characters
capitalize_first(): Capitalise the first letter of a string

Internal (Shiny module implementation)

Shiny module UI/server function pairs and other internal helpers that back the modules above. These aren’t part of the public API and are listed here only so the reference index build succeeds; see the package vignette for the supported way to build and combine modules.

COLORBLIND_PALETTE: shinyngs' fixed categorical colour palette
ExploratorySummarizedExperiment-class: The ExploratorySummarizedExperiment class
`[`(<ExploratorySummarizedExperimentList>,<ANY>,<missing>,<ANY>) `[`(<ExploratorySummarizedExperimentList>,<numeric>,<missing>,<ANY>) `[`(<ExploratorySummarizedExperimentList>,<logical>,<missing>,<ANY>): The ExploratorySummaizedExperimentList class
a11yControl(): Give a terse control an accessible name and a hover/focus tooltip
addColorbyMenu(): Colour points by a chosen variable, with a plotly dropdown to switch it
addColoredPoints(): Colour points by a single variable, highlighting labelled rows
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
annotateDifferentialTable(): Annotate a differential-scatter table with colorby and label columns
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
barplot(): Server function of the barplot module
barplotInput(): Input function of the barplot module
barplotOutput(): Output function of the barplot module
bookmarkedInputValue(): Read a bookmarked input value from a restore state
box_summary(): Summarise a vector into the statistics a box plot needs
boxplot(): The server function of the boxplot module
boxplotInput(): The input function of the boxplot module
boxplotOutput(): The output function of the boxplot module
calculatePCAFractionExplained(): Extract the percent variance from a PCA analysis
cardinalNumericField(): Make a numeric field with selectable associated cardinality (>, < ..).
categorycountplot(): The server function of the categorycountplot module
categorycountplotInput(): The input function of the categorycountplot module
categorycountplotOutput(): The output function of the categorycountplot module
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.
clustering(): The server function of the clustering module
clusteringInput(): The input function of the clustering module
clusteringOutput(): The output function of the clustering module
colormaker(): The output function of the colorby module
colormakerInput(): The input function of the colorby module
combinedAnnotationColors(): Build one shared color palette across every value in an annotation data frame
compile_contrast_data(): Compile contrast stats for inclusion in shinyngs
configureBookmarking(): Configure URL bookmarking for the top-level session
contrasts(): The server function of the contrasts module
contrastsInput(): The input function of the contrasts module
contrastsOutput(): The output function of the contrasts module
defaultGroupvar(): Resolve the default grouping variable for an experiment list
dendro(): The server function of the dendrogram module
dendroInput(): The input function of the dendrogram module
dendroOutput(): The output function of the dendro module
detailSamples() detailFeatures() detailAssays() detailGroups() detailContrasts() detailGenesets(): Detail-drawer builders, one per tile
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
differentialscatterInput(): Shared UI input scaffolding for the differential-scatter plot modules
differentialscatterLogic(): Shared server logic for the differential-scatter plot modules
differentialscatterOutput(): Shared output scaffolding for the differential-scatter plot modules
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
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
fieldSets(): Create sets of fields for display
finiteAxisRange(): Finite x/y bounds of a differential-scatter table
fixedEffectsModelMatrix(): Build a model matrix from the fixed-effects part of a formula
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
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
geneModelBiotypeColors(): Default color table for Ensembl transcript biotypes, used to color the full transcript catalog track loaded by the gene module's gene model view
geneModelGenomeInfo(): Map an Ensembl species name to an igv.js genome build and, where known, a hosted Ensembl GFF3 annotation for that build
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
groupby(): The server function of the groupby module
groupbyInput(): The UI function of the groupby module
heatmap(): The server function of the heatmap module
heatmapInput(): The input function of the heatmap module
heatmapOutput(): The output function of the heatmap module
homeNavTargets(): Shared tab-panel values targeted from the landing page
homeTab(): Build the landing ("Home") tab for a full shinyngs application
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
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
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.
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
modalServer(): The server function of the modal module
moduleLayout(): Lay out a module's controls beside its output
moduleMain(): Assemble a module's main-panel content
navLink(): Build a link that activates a navbar tab client-side
pca(): The server function of the pca module
pcaInput(): The input function of the pca module
pcaOutput(): The output function of the pca module
pcLabels(): "PC1", "PC2", ... labels for the leading n components
plotdownload(): The server function of the gene set module
plotdownloadInput(): The input function of the gene plotdownload module
readreports(): Server function of the readreports module
readreportsInput(): Input function of the readreports module
readreportsOutput(): Output function of the readreports module
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
sampleselect(): The server function of the sampleselect module
sampleselectInput(): The UI input function of the sampleselect module
scatterplot(): Server function for the scatterplot module
scatterplotInput(): Input function for the scatterplot module
scatterplotOutput(): Output function for the scatterplot module
scatterplotcontrols(): Server function for scatterplotcontrols module
scatterplotcontrolsInput(): Input function for scatterplotcontrols module
selectFoldchangeLines(): Select which fold change plot threshold lines to draw
selectMaLines(): Select which MA plot threshold lines to draw
selectVolcanoLines(): Select which volcano plot threshold lines to draw
selectmatrix(): The server function of the selectmatrix module
selectmatrixInput(): The UI input function of the selectmarix module
shinyngs-package shinyngs: Interactive downstream analysis with ShinyNGS.
shinyngsPageNavbar(): Build the top-level bslib page shell shared by the app modules
shinyngsPlotlyConfig(): Apply shinyngs' shared plotly toolbar configuration
shinyngsSpinnerColor(): Accent colour for loading spinners
simpleApp(): Produce a simple app with controls and layout for a single module, in a shiny sideBarLayout().
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
splitAnnotationLegend(): Replace heatmaply's combined annotation legend with one split by variable
summarisematrix(): The server function of the summarisematrix module
summarisematrixInput(): The input function of the summarizematrix module
summaryTileSpecs(): Assemble the summary tile specifications for an experiment list
summaryTileTag(): Build a single clickable summary tile
summarytiles(): The server function of the summarytiles module
summarytilesInput(): The UI input function of the summarytiles module
summarytilesOutput(): The output function of the summarytiles module
topgeneAnnotationData(): Build the per-facet annotation data frame used by static_topgene_boxplots
topgeneAnnotationVector(): Build a per-gene annotation vector, in genes order, for interactive_topgene_boxplots
topgeneboxplot(): The server function of the topgeneboxplot module
topgeneboxplotInput(): The input function of the topgeneboxplot module
topgeneBoxplotData(): Reshape an assay matrix into long form for static_topgene_boxplots
topgeneBoxplotLayout(): Compute the total plot height and inter-row margin fraction needed to lay out n_genes faceted boxplots over ncol columns without rows overlapping
topgeneboxplotOutput(): The output function of the topgeneboxplot module
topgeneRankOptions(): Ranking options from topgene_rank_options whose contrast-table column is actually present
topgeneTransformAssay(): Log2-transform an assay matrix and subset/order it to the requested genes
upset(): The server function of the upset module
upsetInput(): The input function of the upset module
upsetOutput(): The output function of the upset module
upset_calculate_intersections(): Compute set intersections and sizes for an UpSet-style plot
upset_filter_intersections_by_order(): Drop intersections involving fewer than a minimum number of sets
upset_grid_plot(): Make the grid of points indicating set membership in intersections
upset_intersect_size_chart(): Make the bar chart illustrating intersect size
upset_set_size_chart(): Make the bar chart illustrating set sizes
validateFormulaBasedContrast(): Validate a formula-based contrast string against fixed-effect coefficients
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