---
title: >
  The `iSEEfier` User's Guide
author:
- name: Najla Abassi
  affiliation:
  - Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz
  email: najla.abassi@uni-mainz.de
- name: Federico Marini
  affiliation:
  - Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz
  - Research Center for Immunotherapy (FZI), Mainz
  email: marinif@uni-mainz.de
date: "`r BiocStyle::doc_date()`"
output:
  BiocStyle::html_document:
    toc: true
    toc_float: true
vignette: >
  %\VignetteIndexEntry{iSEEfier_userguide}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
  %\VignettePackage{iSEEfier}

---
```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  error    = FALSE,
  warning  = FALSE,
  eval     = TRUE,
  message  = FALSE
)
```

# Introduction {#introduction}

This vignette describes how to use the `r BiocStyle::Biocpkg("iSEEfier")`
package to configure various initial states of iSEE instances, in order to
simplify the task of visualizing single-cell RNA-seq, bulk RNA-seq data, or even
your proteomics data in `r BiocStyle::Biocpkg("iSEE")`.
In the remainder of this vignette, we will illustrate the main features of `r
BiocStyle::Biocpkg("iSEEfier")` on a publicly available dataset from Baron et
al. "A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals
Inter- and Intra-cell Population Structure", published in Cell Systems in 2016.
[doi:10.1016/j.cels.2016.08.011](https://doi.org/10.1016/j.cels.2016.08.011).
The data is made available via the `r BiocStyle::Biocpkg("scRNAseq")`
Bioconductor package. We'll simply use the mouse dataset, consisting of islets
isolated from five C57BL/6 and ICR mice.
# Getting started {#gettingstarted}
To install `r BiocStyle::Biocpkg("iSEEfier")` package, we start R and enter:

```{r install, eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("iSEEfier")
```

Once installed, the package can be loaded and attached to the current workspace
as follows:

```{r setup}
library("iSEEfier")
```

# Create an initial state for gene expression visualization using `iSEEinit()`

When we have all input elements ready, we can create an `iSEE` initial state by
running:

```{r runfunc, eval=FALSE}
iSEEinit(sce = sce_obj,
         features = feature_list,
         reddim.type = reduced_dim,
         clusters = cluster,
         groups = group,
         add_markdown_panel = FALSE)
```

To configure the initial state of our `iSEE` instance using `iSEEinit()`, we
need five parameters:

1.  `sce` : A `SingleCellExperiment` object. This object stores information of
different quantifications (counts, log-expression...), dimensionality reduction
coordinates (t-SNE, UMAP...), as well as some metadata related to the samples
and features.
We'll start by loading the `sce` object:

```{r loaddata}
library("scRNAseq")
sce <- BaronPancreasData('mouse')
sce
```

Let's add the normalized counts

```{r logNorm}
library("scuttle")
sce <- logNormCounts(sce)
```

Now we can add different dimensionality reduction coordinates

```{r reddim}
library("scater")
sce <- runPCA(sce)
sce <- runTSNE(sce)
sce <- runUMAP(sce)
```

Now our `sce` is ready, we can move on to the next argument.

2.  `features` : which is a vector or a dataframe containing the genes/features
of interest.
Let's say we would like to visualize the expression of some genes that were
identified as marker genes for different cell population.

```{r genelist}
gene_list <- c("Gcg", # alpha
               "Ins1") # beta
```

3.  `reddim_type` : In this example we decided to plot our data as a t-SNE plot.

```{r reddim-type}
reddim_type <- "TSNE"
```

4.  `clusters` : Now we specify what clusters/cell-types/states/samples we would
like to color/split our data with

```{r cluster-id}
# cell populations
cluster <- "label" #the name should match what's in the colData names
```

5.  `groups` : Here we can add the groups/conditions/cell-types

```{r group-id}
# ICR vs C57BL/6
group <- "strain" #the name should match what's in the colData names
```

We can choose to include in this initial step a `MarkdownBoard` by setting the arguments
`add_markdown_panel` to `TRUE`.
At this point, all the elements are ready to be transferred into `iSEEinit()`

```{r initial1}
initial1 <- iSEEinit(sce = sce,
                    features = gene_list,
                    clusters = cluster,
                    groups = group,
                    add_markdown_panel = TRUE)
```

In case our `features` parameter was a data.frame, we could assign the name of the column containing the features to the `gene_id` parameter.

Now we are one step away from visualizing our list of genes of interest. All
that's left to do is to run `iSEE` with the initial state created with
`iSEEinit()`

```{r iSEEviz1, eval=FALSE}
library("iSEE")
iSEE(sce, initial= initial1)
```

This instance, generated with `iSEEinit()`, returns a combination of panels,
linked to each other, with the goal of visualizing the expression of certain
marker genes in each cell population/group:

-   A `ReducedDimensionPlot`, `FeatureAssayPlot` and `RowDataTable` for each single gene in `features`.
-   A `ComplexHeatmapPlot` with all genes in `features`
-   A `ColumnDataPlot` panel
-   A `MarkdownBoard` panel

# Create an initial state for feature sets exploration using `iSEEnrich()`

Sometimes it is interesting to look at some specific feature sets and the
associated genes. That's when the utility of `iSEEnrich` becomes apparent. We
will need 4 elements to explore feature sets of interest:

-   `sce`: A SingleCellExperiment object
-   `collection`: A character vector specifying the gene set collections of interest (it is possible to use GO or KEGG terms)
-   `gene_identifier`: A character string specifying the identifier to use to extract gene IDs for the organism package. This can be **"ENS"** for ENSEMBL ids, **"SYMBOL"** for gene names...
-   `organism`: A character string of the `org.*.eg.db` package to use to extract mappings of gene sets to gene IDs.
-   `reddim_type`: A string vector containing the dimensionality reduction type
-   `clusters`: A character string containing the name of the clusters/cell-type/state...(as listed in the colData of the sce)
-   `groups`: A character string of the groups/conditions...(as it appears in the colData of the sce)


```{r set-param}
GO_collection <- "GO"
Mm_organism <- "org.Mm.eg.db"
gene_id <- "SYMBOL"
cluster <- "label"
group <- "strain"
reddim_type <- "PCA"
```

Now let's create this initial setup for `iSEE` using `iSEEnrich()`

```{r initial2}
results <- iSEEnrich(
  sce = sce,
  collection = GO_collection,
  gene_identifier = gene_id,
  organism = Mm_organism,
  clusters = cluster,
  reddim_type = reddim_type,
  groups = group
)
```

`iSEEnrich` will specifically return a list with the updated `sce` object and
its associated `initial` configuration. To start the `iSEE` instance we run:

```{r iSEEviz2,  eval=FALSE}
iSEE(results$sce, initial = results$initial)
```

# Create an initial state for marker gene exploration using `iSEEmarker()`

In many cases, we are interested in determining the identity of our clusters, or further subset our cells types. That's where `iSEEmarker()` comes in handy. Similar to `iSEEinit()`, we need the following parameters:

- `sce`: a `SingleCellExperiment` object
- `clusters`: the name of the clusters/cell-type/state
- `groups`: the groups/conditions
- `selection_plot_format`: the class of the panel that we will be using to select the clusters of interest.

```{r initial3}
initial3 <- iSEEmarker(
  sce = sce,
  clusters = cluster,
  groups = group,
  selection_plot_format = "ColumnDataPlot")
```

This function returns a list of panels, with the goal of visualizing the expression of
marker genes selected from the `DynamicMarkerTable` in each cell cell type. Unlike `iSEEinit()`, which requires us to specify a list of genes, `iSEEmarker()` utilizes the `DynamicMarkerTable` that performs statistical testing through the `findMarkers()` function from the `r BiocStyle::Biocpkg("scran")` package.
To start exploring the marker genes of each cell type with `iSEE`, we run:

```{r iSEEviz3,  eval=FALSE}
iSEE(sce, initial = initial3)
```

# Visualize a preview of the initial configurations with `view_initial_tiles()`

Previously, we successfully generated three distinct initial configurations for
iSEE. However, understanding the expected content of our iSEE instances is not
always straightforward. That's when we can use `view_initial_tiles()`.
We only need as an input the initial configuration to obtain a graphical
visualization of the expected the corresponding `iSEE` instance:

```{r panelgraph}
library(ggplot2)
view_initial_tiles(initial = initial1)
view_initial_tiles(initial = results$initial)
```

# Visualize network connections between panels with `view_initial_network()`

As some of these panels are linked to each other, we can visualize these
networks with `view_initial_network()`. Similar to `iSEEconfigviewer()`, this
function takes the initial setup as input:
This function always returns the `igraph` object underlying the visualizations
that can be displayed as a side effect.

```{r networkviz}
library("igraph")
library("visNetwork")
g1 <- view_initial_network(initial1, plot_format = "igraph")
g1
initial2 <- results$initial
g2 <- view_initial_network(initial2, plot_format = "visNetwork")
```

# Merge different initial configurations with `glue_initials()`

Sometimes, it would be interesting to merge different `iSEE` initial
configurations to visualize all different panel in the same `iSEE` instance.

```{r glueconfig}
merged_config <- glue_initials(initial1,initial2)
```

We can then preview the content of this initial configuration

```{r preview}
view_initial_tiles(merged_config)
```

# Related work

The idea of launching `iSEE()` with some specific configuration is not entirely
new, and it was covered in some use cases by the `mode_` functions available in
the `r BiocStyle::Biocpkg("iSEEu")` package.\ There, the user has access to the
following:

-   `iSEEu::modeEmpty()` - this will launch `iSEE` without any panels, and let you build up the configuration from the scratch. Easy to start, easy to build.
-   `iSEEu::modeGating()` - this will open `iSEE` with multiple chain-linked FeatureExpressionPlot panels, just like when doing some in silico gating. This could be a very good fit if working with mass cytometry data.
-   `iSEEu::modeReducedDim()` - `iSEE` will be ready to compare multiple ReducedDimensionPlot panels, which is a suitable option to compare the views resulting from different embeddings (and/or embeddings generated with slightly different parameter configurations).
The `mode`s directly launch an instance of `iSEE`, whereas the functionality in
`r BiocStyle::Biocpkg("iSEEfier")` is rather oriented to obtain more
tailored-to-the-data-at-hand `initial` objects, that can subsequently be passed
as an argument to the `iSEE()` call.
We encourage users to submit suggestions about their "classical ways" of using
`iSEE` on their data - be that by opening an issue or already proposing a Pull
Request on GitHub.

# Session info {.unnumbered}

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