shinyngs: Interactive downstream analysis with ShinyNGS.

In pinin4fjords/shinyngs: Shiny apps for NGS data

Interactive downstream analysis with ShinyNGS.

Description

shinyngs is a package for downstream visualisation of data stored in SummarizedExperiment-like objects, produced as a end-point of bioinformatics analysis workflows.

Details

What follows is technical documentation for the package, use vignette('shinyngs') to get more user-friendly information on package usage.

Principal software dependencies

This package makes use of many packages, and is indebted to their developers. Shiny provides the overall framework that made the current work possible, and Plotly has been key to making the included visualisations as dynamic and useful as they are.

Plotly's R interface has changed markedly between versions, and shinyngs is currently dependent on a version later than the (now somewhat old) version on CRAN. This should therefore be installed from GitHub: devtools::install_github('ropensci/plotly', upgrade_dependencies = FALSE).

Input data structure

shinyngs defines two new data structures. The first, ExploratorySummarizedExperiment simply takes SummarizedExperiment, and adds some slots to allow extra description around experiments. These extra slots are not compulsory, however, and a simple SummarizedExperiment can be converted directly into an ExploratorySummarizedExperiment:

 ese <- as(airway, 'ExploratorySummarizedExperiment') 

Because a single ExploratorySummarizedExperiment is limited to one set of features, ExploratorySummarizedExperimentList was devised to allow incorporation of other feature sets. For example, we might want to visualise expression in terms of both transcripts and genes. ExploratorySummarizedExperimentList is just a list of ExploratorySummarizedExperiments, with some additonal slots pertaining to a study as a whole.

To use shinyngs, data is assumed to be in these formats. I'm not terribly happy with the structure of some of the slots in these objects, and they may be open to 'improvement' in the future.

Example data

An example based on the Zhang et al study of neurons and glia (http://www.jneurosci.org/content/34/36/11929.long) is included in the package, and can be picked apart to further understand the data structure.

Shiny modules

The functionality of shinyngs revolves around Shiny's concept of modules (http://shiny.rstudio.com/articles/modules.html), so this bears some explanation.

Modules allow essentially object-oriented coding for Shiny, and the hiving of of code into namespaces such that it can be re-used in different parts of an application without interfering with itself. shinyngs has many modules that provide various functionalities.

Components

Each module will have server and UI functions that provide processing and UI functionality respectively. For example, the dendro module, which provides sample clustering dengrograms, has dendroInput, which provides user interface components to determine clustering method etc, and dendro, which parses those inputs and calls the appropriate functions to generate a dendrogram. dendroOutput provides elements that display the outputs when they're ready. These functions are all present in dendro.R.

Usage

Any application seeking to create dendrograms need only call dendroInput dendroOutput in the parts of their application where inputs and outputs should appear, and then use callModule (again using the same ID) to activate them.

  dendroInput(ns('dendro'), eselist)
  dendroOutput(ns('dendro'))
  callModule(dendro, 'dendro', eselist) 

These module functions are not currently exported, not currenlty being intended for use outside shinyngs. This may change.

Main functions

Usage of modules defined in shinyngs is envisaged to be predominantly via prepareApp. For most modules, this passes its arguments to simpleApp, which very simply takes its ExploratorySummarizedExperimentList and a module name, and attempts to call the UI and server functions of that module, creating a simple sidebar layout. Taking our dendro app and using the airway example data:

  data(airway, package = 'airway')
  ese <- as(airway, 'ExploratorySummarizedExperiment')
  eselist <- ExploratorySummarizedExperimentList(ese)
  app <- prepareApp('heatmap',eselist)

Other apps, for example rnaseq require more complex layouts and don't use simpleApp.

prepareApp returns list with UI and server applications components. Shiny's shinyApp must then be called to actually run the app: shiny::shinyApp(ui = app$ui, server = app$server).

Deploying to a shiny server

Assuming a ExploratorySummarizedExperimentList has been serialised with link[base]{saveRDS}, the Shiny app can be deployed to a server in a script called 'app.R' with content like this:

  library(shinyngs)
  mydata <- readRDS('data.rds') app <- prepareApp('rnaseq', mydata)
  shiny::shinyApp(app$ui, app$server)

Module list

There are three varieties of module in shinyngs. Top-level modules such as rnaseq provide complex data mining tools pulling together a number of other modules. Some of those sub-modules can also be called stand-alone to make heatmaps or dendrograms, for example. Other modules just provide small components that don't make sense in isolation. This is the full set at the time of writing:

Top-level

rnaseq

Pull together PCA analysis, heat maps, dendgrograms, volcano plots, gene sets etc to make a comprehensive data mining tool.

chipseq

Currenlty a near clone of rnaseq, to be optimised for ChIP-seq in due course.

Stand-alone

These modules can also be called directly with prepareApp:

assaydatatable

Provide access to asay matrices of input object

boxplot

Make quartile/ boxplots

dendro

Make sample-clustering dendgrograms.

dexseqplot

Differential exon usage plot (where relevant slot populated)

dexseqtable

Differential exon usage table (where relevant slot populated)

differentialtable

Differential table showing summarised group values and fold changes etc (where contrasts slot is populated).

experimentaltable

Display colData() output from selected ExploratorySummarizedExperiment

foldchangeplot

Plot mean values of one condition against another (where contrasts slot is populated)

gene

Show expression plots and other available data for selected features

genesetanalysistable

Display content of the gene_set_analyses slot for the selected ExploratorySummarizedExperiment

genesetbarcodeplot

Make a barcode plot using selected data and limma's barcodeplot

heatmap

Build heatmaps from selected matrix data. By default this is an expression matrix, but it can also be sample vs sample correlation heatmaps or PCA vs covariate association heatmaps.

maplot

Uses the scatterplot module to plot mean expression vs fold change

pca

Plots 2D or 3D PCA and loading plots based on selected matrix data, using the scatterplot module

readreports

Makes bar plots and tables of read counts data where provided in the read_reports slot of an ExploratorySummarizedExperimentList

rowmetatable

Displays data from the metadata slot of a ExploratorySummarizedExperiment object (accessed via mcols)

volcanoplot

Uses the scatterplot module to plot fold change vs p value (where necessary slots are populated

Component-only

These modules are only valid as components of applications created by other modules:

barplot

Used by readreports, for example. Requires reactive providing input data

contrasts

Provides data on sample group comparisons, using the contrasts slot of the input object (where available)

geneselect

Provides selection filters for assay matrix rows. Used mainly by the selectmatrix module

genesetselect

Uses Selectize to provide an autocomplete field to select from available gene sets (where provided in the gene_sets slot)

groupby

Provides a UI element to choose from the group_vars in a SummarizedExperment. Useful for coloring in a PCA etc

labelselectfield

This module provides an input which allows filtering on the basis of row IDs, labels, or other data in the metadata slot of an ExploratorySummarizedExperiment

modal

uses modals from shinyBS to create overlaid text for the current panel which displays when a link is clicked

plotdownload

Provides a download button for displayed plots

sampleselect

Allows a subset of columns to be selected from the selected assay matrix

scatterplot

A generic module for producing scatter plots using Plotly's plot_ly method. Used by multiple other modules, including foldchangeplot and volcanoplot

scatterplotcontrols

A set of controls for scatter plots. Separation of controls in this module allows them to be used in multiple scatter plot instances. For example, both PCA and loading plots can be run off the same set of controls

selectmatrix

Provides functionality central to shinyngs. Uses filtes on experiment and assay, along with sampleselect and geneselect, to select parts of input matrices for use by most other shinyngs modules

simpletable

A useful generic module that takes a reactive which returns a matrix, and both displays that table and produces a download button

summarizematrix

Module which takes a matrix and a factor which groups columns, and summarises by a supplied method, mean by default

pinin4fjords/shinyngs documentation built on Feb. 28, 2024, 10:19 a.m.