---
title: Universe of iSEE panels
author:
- name: Kevin Rue-Albrecht
  affiliation: 
  - &id1 Kennedy Institute of Rheumatology, University of Oxford,
    Headington, Oxford OX3 7FY, UK.
  email: kevin.rue-albrecht@kennedy.ox.ac.uk
- name: Federico Marini
  affiliation: 
  - &id2 Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz
  - Center for Thrombosis and Hemostasis (CTH), Mainz
  email: marinif@uni-mainz.de
- name: Charlotte Soneson
  affiliation: 
  - &id3 Friedrich Miescher Institute for Biomedical Research, Basel
  - SIB Swiss Institute of Bioinformatics
  email: charlottesoneson@gmail.com
- name: Aaron Lun
  email: infinite.monkeys.with.keyboards@gmail.com  
date: "`r BiocStyle::doc_date()`"
package: iSEEu
output: BiocStyle::html_document
vignette: >
  %\VignetteIndexEntry{Panel universe}
  %\VignetteEncoding{UTF-8}  
  %\VignettePackage{iSEEu}
  %\VignetteKeywords{GeneExpression, RNASeq, Sequencing, Visualization, QualityControl, GUI}
  %\VignetteEngine{knitr::rmarkdown}
bibliography: iSEEu.bib  
---

```{r, echo=FALSE}
knitr::opts_chunk$set(error=FALSE, warning=FALSE, message=FALSE)
library(BiocStyle)
```

```{r, eval=!exists("SCREENSHOT"), include=FALSE}
SCREENSHOT <- function(x, ...) knitr::include_graphics(x)
```

# Overview

The `r Biocpkg("iSEE")` package [@iSEE-2018] provides a general and flexible framework for interactively exploring `SummarizedExperiment` objects.
However, in many cases, more specialized panels are required for effective visualization of specific data types.
The `r Biocpkg("iSEEu")` package implements a collection of such dedicated panel classes that work directly in the `iSEE` application and can smoothly interact with other panels.
This allows users to quickly parametrize bespoke apps for their data to address scientific questions of interest.
We first load in the package:

```{r}
library(iSEEu)
```

All the panels described in this document can be deployed by simply passing them into the `iSEE()` function via the `initial=` argument, as shown in the following examples.

# Differential expression plots

To demonstrate the use of these panels,
we will perform a differential expression analysis on the `r Biocpkg("airway")` dataset with the `r Biocpkg("edgeR")` package.
We store the resulting statistics in the `rowData` of the `SummarizedExperiment` so that it can be accessed by `iSEE` panels.

```{r}
library(airway)
data(airway)

library(edgeR)
y <- DGEList(assay(airway), samples=colData(airway))
y <- y[filterByExpr(y, group=y$samples$dex),]
y <- calcNormFactors(y)

design <- model.matrix(~dex, y$samples)
y <- estimateDisp(y, design)
fit <- glmQLFit(y, design)
res <- glmQLFTest(fit, coef=2)

tab <- topTags(res, n=Inf)$table
rowData(airway) <- cbind(rowData(airway), tab[rownames(airway),])
```

The `MAPlot` class creates a MA plot, i.e., with the log-fold change on the y-axis and the average expression on the x-axis.
Features with significant differences in each direction are highlighted and counted on the legend.
Users can vary the significance threshold and apply _ad hoc_ filters on the log-fold change.
This is a subclass of the `RowDataPlot` so points can be transmitted to other panels as multiple row selections.
Instances of this class are created like:

```{r}
ma.panel <- MAPlot(PanelWidth=6L)
app <- iSEE(airway, initial=list(ma.panel))
```

```{r, echo=FALSE}
SCREENSHOT("screenshots/ma.png")
```

The `VolcanoPlot` class creates a volcano plot with the log-fold change on the x-axis and the negative log-p-value on the y-axis.
Features with significant differences in each direction are highlighted and counted on the legend.
Users can vary the significance threshold and apply _ad hoc_ filters on the log-fold change.
This is a subclass of the `RowDataPlot` so points can be transmitted to other panels as multiple row selections.
Instances of this class are created like:

```{r}
vol.panel <- VolcanoPlot(PanelWidth=6L)
app <- iSEE(airway, initial=list(vol.panel))
```

```{r, echo=FALSE}
SCREENSHOT("screenshots/volcano.png")
```

The `LogFCLogFCPlot` class creates a scatter plot of two log-fold changes from different DE comparisons.
This allows us to compare DE results on the same dataset - or even from different datasets, as long as the row names are shared.
Users can vary the significant threshold used to identify DE genes in either or both comparisons.
This is a subclass of the `RowDataPlot` so points can be transmitted to other panels as multiple row selections.
Instances of this class are created like:

```{r}
# Creating another comparison, this time by blocking on the cell line
design.alt <- model.matrix(~cell + dex, y$samples)
y.alt <- estimateDisp(y, design.alt)
fit.alt <- glmQLFit(y.alt, design.alt)
res.alt <- glmQLFTest(fit.alt, coef=2)

tab.alt <- topTags(res.alt, n=Inf)$table
rowData(airway) <- cbind(rowData(airway), alt=tab.alt[rownames(airway),])

lfc.panel <- LogFCLogFCPlot(PanelWidth=6L, YAxis="alt.logFC", 
    YPValueField="alt.PValue")
app <- iSEE(airway, initial=list(lfc.panel))
```

```{r, echo=FALSE}
SCREENSHOT("screenshots/logfclogfc.png")
```

# Dynamically recalculated panels

To demonstrate, we will perform a quick analysis of a small dataset from the `r Biocpkg("scRNAseq")` package.
This involves computing normalized expression values and low-dimensional results using the `r Biocpkg("scater")` package.

```{r}
library(scRNAseq)
sce <- ReprocessedAllenData(assays="tophat_counts")

library(scater)
sce <- logNormCounts(sce, exprs_values="tophat_counts")
sce <- runPCA(sce, ncomponents=4)
sce <- runTSNE(sce)
```

The `DynamicReducedDimensionPlot` class creates a scatter plot with a dimensionality reduction result, namely principal components analysis (PCA), $t$-stochastic neighbor embedding ($t$-SNE) or uniform manifold and approximate projection (UMAP).
It does so dynamically on the subset of points that are selected in a transmitting panel,
allowing users to focus on finer structure when dealing with a heterogeneous population.
Calculations are performed using relevant functions from the `r Biocpkg("scater")` package.

```{r}
# Receives a selection from a reduced dimension plot.
dyn.panel <- DynamicReducedDimensionPlot(Type="UMAP", Assay="logcounts",
    ColumnSelectionSource="ReducedDimensionPlot1", PanelWidth=6L)

# NOTE: users do not have to manually create this, just 
# copy it from the "Panel Settings" of an already open app.
red.panel <- ReducedDimensionPlot(PanelId=1L, PanelWidth=6L,
    BrushData = list(
        xmin = -45.943, xmax = -15.399, ymin = -58.560, 
        ymax = 49.701, coords_css = list(xmin = 51.009, 
            xmax = 165.009, ymin = 39.009, 
            ymax = 422.009), coords_img = list(xmin = 66.313, 
            xmax = 214.514, ymin = 50.712, 
            ymax = 548.612), img_css_ratio = list(x = 1.300, 
            y = 1.299), mapping = list(x = "X", y = "Y"), 
        domain = list(left = -49.101, right = 57.228, 
            bottom = -70.389, top = 53.519), 
        range = list(left = 50.986, right = 566.922, 
            bottom = 603.013, top = 33.155), 
        log = list(x = NULL, y = NULL), direction = "xy", 
        brushId = "ReducedDimensionPlot1_Brush", 
        outputId = "ReducedDimensionPlot1"
    )
)

app <- iSEE(sce, initial=list(red.panel, dyn.panel))
```

```{r, echo=FALSE}
SCREENSHOT("screenshots/dynreddim.png")
```

The `DynamicMarkerTable` class dynamically computes basic differential statistics comparing assay values across groups of multiple selections in a transmitting panel.
If only the active selection exists in the transmitting panel, a comparison is performed between the points in that selection and all unselected points.
If saved selections are present, pairwise comparisons between the active selection and each saved selection is performed and the results are combined into a single table using the `findMarkers()` function from `r Biocpkg("scran")`.

```{r}
diff.panel <- DynamicMarkerTable(PanelWidth=8L, Assay="logcounts",
    ColumnSelectionSource="ReducedDimensionPlot1",)

# Recycling the reduced dimension panel above, adding a saved selection to
# compare to the active selection.
red.panel[["SelectionHistory"]] <- list(
    BrushData = list(
        xmin = 15.143, xmax = 57.228, ymin = -40.752, 
        ymax = 25.674, coords_css = list(xmin = 279.009, 
            xmax = 436.089, ymin = 124.009, 
            ymax = 359.009), coords_img = list(xmin = 362.716, 
            xmax = 566.922, ymin = 161.212, 
            ymax = 466.712), img_css_ratio = list(x = 1.300, 
            y = 1.299), mapping = list(x = "X", y = "Y"), 
        domain = list(left = -49.101, right = 57.228, 
            bottom = -70.389, top = 53.519), 
        range = list(left = 50.986, right = 566.922, 
            bottom = 603.013, top = 33.155), 
        log = list(x = NULL, y = NULL), direction = "xy", 
        brushId = "ReducedDimensionPlot1_Brush", 
        outputId = "ReducedDimensionPlot1"
    )
)
red.panel[["PanelWidth"]] <- 4L # To fit onto one line.

app <- iSEE(sce, initial=list(red.panel, diff.panel))
```

```{r, echo=FALSE}
SCREENSHOT("screenshots/diffstat.png")
```

# Feature set table

The `FeatureSetTable()` class is a bit unusual in that its rows do not correspond to any dimension of the `SummarizedExperiment`.
Rather, each row is a feature set (e.g., from GO or KEGG) that, upon click, transmits a multiple row selection to other panels.
The multiple selection consists of all rows in the chosen feature set,
allowing users to identify the positions of all genes in a pathway of interest on, say, a volcano plot.
This is also a rare example of a panel that only transmits and does not receive any selections from other panels.

```{r}
setFeatureSetCommands(createGeneSetCommands(identifier="ENSEMBL"))

gset.tab <- FeatureSetTable(Selected="GO:0002576", 
    Search="platelet", PanelWidth=6L)

# This volcano plot will highlight the genes in the selected gene set.
vol.panel <- VolcanoPlot(RowSelectionSource="FeatureSetTable1",
    SelectionEffect="Color", PanelWidth=6L)

app <- iSEE(airway, initial=list(gset.tab, vol.panel))
```

```{r, echo=FALSE}
SCREENSHOT("screenshots/geneset.png", delay=30)
```

# App modes

`r Biocpkg("iSEEu")` contains a number of "modes" that allow users to conveniently load an `iSEE` instance in one of several common configurations:

- `modeEmpty()` will launch an empty app, i.e., with no panels.
This is occasionally useful to jump to the landing page where a user can then upload a `SummarizedExperiment` object.
- `modeGating()` will launch an app with multiple feature assay panels that are linked to each other.
This is useful for applying sequential restrictions on the data, equivalent to gating in a flow cytometry experiment.
-  `modeReducedDim()` will launch an app with multiple reduced dimension plots.
This is useful for examining different views of large high-dimensional datasets (e.g., single-cell studies).

# Contributing to `r Biocpkg("iSEEu")`

If you want to contribute to the development of the `r Biocpkg("iSEEu")` package, here is a quick step-by-step guide:

- Fork the `iSEEu` repository from GitHub (https://github.com/iSEE/iSEEu) and clone it locally.

```
git clone https://github.com/[your_github_username]/iSEEu.git
```

- Add the desired new files - start from the `R` folder, then document via `roxygen2` - and push to your fork. 
  As an example you can check out to understand how things are supposed to work, there are several modes already defined in the `R/` directory. 
  A typical contribution could include e.g. a function defining an `r Biocpkg("iSEE")` mode, named `modeXXX`, where `XXX` provides a clear representation of the purpose of the mode. 
  Please place each mode in a file of its own, with the same name as the function. 
  The function should be documented (including an example), and any required packages should be added to the `DESCRIPTION` file. 
  
- Once your `mode`/function is done, consider adding some information in the package.
  Some examples might be a screenshot of the mode in action (to be placed in the folder `inst/modes_img`), and a well-documented example use case (maybe an entry in the `vignettes` folder). Also add yourself as a contributor (`ctb`) to the `DESCRIPTION` file.

- Make a pull request to the original repo - the GitHub site offers a practical framework to do so, enabling comments, code reviews, and other goodies.
  The `r Biocpkg("iSEE")` core team will evaluate the contribution and get back to you!

That's pretty much it!

#### Using example data sets {-}

Example data sets can often be obtained from an `r Biocpkg("ExperimentHub")` package (e.g. from the `r Biocpkg("scRNAseq")` package for single-cell RNA-sequencing data), and should not be added to the `r Biocpkg("iSEEu")` package.
  
#### Documenting, testing, coding style and conventions {-}

- If possible, please consider adding an example in the dedicated Roxygen preamble to show how to run each function
- If possible, consider adding one or more unit tests - we use the `testthat` framework

We do follow some guidelines regarding the names given to variables, please abide to these for consistency with the rest of the codebase.
Here are a few pointers:

- Keep the indentation as it is in the initial functions already available (4-spaces indentation).
- If writing text (e.g. in the vignette), please use one sentence per line - this makes `git diff` operations easier to check.
- When choosing variable names, try to keep the consistency with what already is existing:
  - `camelCase` for modes and other functions
  - `.function_name` for internals
  - `PanelClassName` for panels
  - `.genericFunction` for the API
  - `.scope1.scope2.name` for variable names in the cached info

If you intend to understand more in depth the internals of the `r Biocpkg("iSEE")` framework, consider checking out the bookdown resource we put together at https://isee.github.io/iSEE-book/

#### Looking for constants within `r Biocpkg("iSEE")` {-}

Many of the "global" variables that are used in several places in `r Biocpkg("iSEE")` are defined in the [constants.R](https://github.com/iSEE/iSEE/blob/master/R/constants.R) script in `r Biocpkg("iSEE")`.
We suggest to refer to those constants by their actual value rather than their internal variable name in downstream panel code.
Both constant variable names and values may change at any time, but we will only announce changes to the constant value.

#### What if I need a custom panel type? {-}

In addition to the eight standard panel types, custom panels are easily accommodated within `r Biocpkg("iSEE")` applications. 
For a guide, see the corresponding [vignette](https://bioconductor.org/packages/release/bioc/vignettes/iSEE/inst/doc/custom.html). 
For examples, see [this repo](https://github.com/iSEE/iSEE_custom).

#### Where can I find a comprehensive introduction to `r Biocpkg("iSEE")`? {-}

The `r Biocpkg("iSEE")` package contains several vignettes detailing the main functionality. 
You can also take a look at this [workshop](https://iSEE.github.io/iSEEWorkshop2019/index.html). 
A compiled version from the Bioc2019 conference (based on Bioconductor release 3.10) is available [here](http://biocworkshops2019.bioconductor.org.s3-website-us-east-1.amazonaws.com/page/iSEEWorkshop2019__iSEE-lab/).

# Session information {-}

```{r}
sessionInfo()
```

# References {-}
