---
title: "Gene set co-regulation analysis tutorial"
output: 
    rmarkdown::html_vignette:
        toc: true
vignette: >
  %\VignetteIndexEntry{Gene set co-regulation analysis tutorial}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

```{r echo=FALSE}
library(BiocParallel)
register(SerialParam())
```

This vignette describes GESECA (gene set co-regulation analysis): a method
to identify gene sets that have high gene correlation.
We will show how GESECA can be used to find regulated pathways
in multi-conditional data, where there is no obvious contrast that 
can be used to rank genes for GSEA analysis.
As examples we will consider a time course microarray experiment 
and a spatial transcriptomics dataset.

## Overiew of GESECA method

GESECA takes as an input:

* *E* - gene expression matrix, where rows and columns correspond to genes and samples respectively.
* *P* - list of gene sets (i.e. 
[hallmark gene sets](http://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#H)).

**Note**: genes identifier type should be the same for both elements of *P* and for row names of matrix *E*.

By default, GESECA method performs centering for rows of the matrix *E*. 
So, after that, the gene values are assumed to have zero mean.
Then for each gene set *p* in *P* let us introduce the gene set score in the following form:

```{r eval=FALSE}
score <- sum(colSums(E[p, ])**2) / length(p)
```

This score was inspired by the variance of principal components 
from the principal component analysis (PCA).
Therefore, the given score can be viewed in terms of explained variance by the gene set *p*.
Geometrically, this can be considered as an embedding of samples into 
a one-dimensional space, given by a unit vector in which nonzero 
positions correspond to genes from gene set *p*.

In the case of row-centered matrix *E* the variance of 
highly correlated genes is summed up to a higher score.
While the genes that are not correlated cancel each other and the total
gene set variance is low.
See the toy example:

![Toy example of GESECA score calculation](geseca-vignette-score-toy-example.png){width=90%}

Another major feature of the proposed score is that it does not require 
an explicit sample annotation or a contrast.
As the result, GESECA can be applied to various types of sequencing technologies: RNA-seq, single-cell sequencing, spatial RNA-seq, etc.

To assess statistical significance for a given gene set *p* we calculate 
an empirical P-value by using gene permutations.
The definition of the P-value is given by the following expression:
\[
    \mathrm{P} \left(\text{random score} \geqslant \text{score of p} \right).
\]
The estimation of the given P-value is done by sampling random gene sets 
with the same size as *p* from the row names of matrix *E*.
In practice, the theoretical P-value can be extremely small, 
so we use the adaptive multilevel Markov Chain Monte Carlo scheme,
that we used previously in `fgseaMultilevel` procedure.
For more details, see the [preprint](https://www.biorxiv.org/content/10.1101/060012v3).

## Analysis of time course data

In the first example we will consider a time course data of Th2 activation
from the dataset GSE200250.

First, let prepare the dataset. We load it from Gene Expression Omnibus,
apply log and quantile normalization and filter lowly expressed genes.

```{r message=FALSE}
library(GEOquery)
library(limma)

gse200250 <- getGEO("GSE200250", AnnotGPL = TRUE)[[1]]

es <- gse200250
es <- es[, grep("Th2_", es$title)]
es$time <- as.numeric(gsub(" hours", "", es$`time point:ch1`))
es <- es[, order(es$time)]

exprs(es) <- normalizeBetweenArrays(log2(exprs(es)), method="quantile")

es <- es[order(rowMeans(exprs(es)), decreasing=TRUE), ]
es <- es[!duplicated(fData(es)$`Gene ID`), ]
rownames(es) <- fData(es)$`Gene ID`
es <- es[!grepl("///", rownames(es)), ]
es <- es[rownames(es) != "", ]

fData(es) <- fData(es)[, c("ID", "Gene ID", "Gene symbol")]

es <- es[head(order(rowMeans(exprs(es)), decreasing=TRUE), 12000), ]
head(exprs(es))
```


Then we obtain the pathway list. Here we use Hallmarks
collection from MSigDB database.


```{r}
library(msigdbr)
pathwaysDF <- msigdbr(species="mouse", collection="H")
pathways <- split(as.character(pathwaysDF$ncbi_gene), pathwaysDF$gs_name)
```

Now we can run GESECA analysis:

```{r message=FALSE}
library(fgsea)
set.seed(1)
gesecaRes <- geseca(pathways, exprs(es), minSize = 15, maxSize = 500)
```

The resulting table contain GESECA scores and the corresponding P-values:
```{r}
head(gesecaRes, 10)
```

We can plot gene expression profile of HALLMARK_E2F_TARGETS pathway and see
that these genes are strongly activated at 24 hours time point:


```{r fig.width=10, fig.height=4, out.width="100%"}
plotCoregulationProfile(pathway=pathways[["HALLMARK_E2F_TARGETS"]], 
                        E=exprs(es), titles = es$title, conditions=es$`time point:ch1`)
```

Hypoxia genes have slightly different profile, getting activated around 48 hours:


```{r fig.width=10, fig.height=4, out.width="100%"}
plotCoregulationProfile(pathway=pathways[["HALLMARK_HYPOXIA"]], 
                        E=exprs(es), titles = es$title, conditions=es$`time point:ch1`)


```

To get an overview of the top pathway patterns we can use `plotGesecaTable`
function:

```{r fig.width=10, fig.height=6, out.width="100%"}
plotGesecaTable(gesecaRes |> head(10), pathways, E=exprs(es), titles = es$title)
```

When the expression matrix contains many samples, a PCA-reduced expression matrix
can be used instead of the full matrix to improve the performance. 
Let reduce the sample space from `r ncol(es)` to 10 dimensions, preserving as much gene variation as possible.

```{r}
E <- t(base::scale(t(exprs(es)), scale=FALSE))
pcaRev <- prcomp(E, center=FALSE)
Ered <- pcaRev$x[, 1:10]
dim(Ered)
```

Now we can run GESECA on the reduced matrix, however we need to disable automatic centering, as we already have done it before the reduction.

```{r}
set.seed(1)
gesecaResRed <- geseca(pathways, Ered, minSize = 15, maxSize = 500, center=FALSE)
head(gesecaResRed, 10)
```

The scores and P-values are similar to the ones we obtained for the full matrix.

```{r fig.width=4, fig.height=4}
library(ggplot2)
ggplot(data=merge(gesecaRes[, list(pathway, logPvalFull=-log10(pval))],
                  gesecaResRed[, list(pathway, logPvalRed=-log10(pval))])) +
    geom_point(aes(x=logPvalFull, y=logPvalRed)) +
    coord_fixed() + theme_classic()
```


## Analysis of single-cell RNA-seq

Let us load necessary libraries. We a going to use `Seurat` package for working with singe cell data.

```{r}
suppressMessages(library(Seurat))
```

As an example dataset we will use GSE116240 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116240).
The dataset features single cell RNA sequencing of aortic CD45+ cells 
and foam cells from atherosclerotic aorta and is extensively described 
in the corresponding publication (https://pubmed.ncbi.nlm.nih.gov/30359200/).
We also thank the authors for providing the corresponding Seurat object
used for the publication.

```{r fig.width=8, fig.height=3.5}
obj <- readRDS(url("https://alserglab.wustl.edu/files/fgsea/GSE116240.rds"))
obj

newIds <- c("0"="Adventitial MF",
            "3"="Adventitial MF",
            "5"="Adventitial MF",
            "1"="Intimal non-foamy MF",
            "2"="Intimal non-foamy MF",
            "4"="Intimal foamy MF",
            "7"="ISG+ MF",
            "8"="Proliferating cells",
            "9"="T-cells",
            "6"="cDC1",
            "10"="cDC2",
            "11"="Non-immune cells")

obj <- RenameIdents(obj, newIds)

DimPlot(obj) + ggplot2::coord_fixed()
```

We apply an appropriate normalization (note that we are using 10000 genes, 
which will be later used as a gene universe for the analysis):

```{r}
obj <- SCTransform(obj, verbose = FALSE, variable.features.n = 10000)
```

To speed up the analysis, instead of using the full transformed
gene expression matrix, we will consider only its first 
principal components. Note that a "reverse" PCA should be done: 
the principal components should correspond to linear combinations
of the cells, not linear combinations of the genes as in "normal" PCA.
By default `SCTransform` returns centered gene expression, so we
can run PCA directly.

```{r}
length(VariableFeatures(obj)) # make sure it's a full gene universe of 10000 genes
obj <- RunPCA(obj, assay = "SCT", verbose = FALSE,
                rev.pca = TRUE, reduction.name = "pca.rev",
              reduction.key="PCR_", npcs = 50)

E <- obj@reductions$pca.rev@feature.loadings
```

Following the authors we are going to use KEGG pathway collection.

```{r}
library(msigdbr)

pathwaysDF <- msigdbr(species="mouse", collection="C2", subcollection = "CP:KEGG_LEGACY")
pathways <- split(pathwaysDF$gene_symbol, pathwaysDF$gs_name)
```

Now we can run the analysis (we set `center=FALSE` because we use the 
reduced matrix):


```{r}
set.seed(1)
gesecaRes <- geseca(pathways, E, minSize = 5, maxSize = 500, center = FALSE, eps=1e-100)

head(gesecaRes, 10)
```


Now we can plot profiles of the top pathways (we need to specify the reduction
as we are using the one from the publication):

```{r fig.width=12, fig.height=7, out.width="100%"}
topPathways <- gesecaRes[, pathway] |> head(4)
titles <- sub("KEGG_", "", topPathways)

ps <- plotCoregulationProfileReduction(pathways[topPathways], obj,
                                       title=titles,
                                       reduction="tsne")
cowplot::plot_grid(plotlist=ps[1:4], ncol=2)
```

We can see that inflammatory pathways (e.g. KEGG_LEISHMANIA_INFECTION) are 
more associated with the non-foamy intimal macrophages, which was one of the
main points of the Kim et al. Another pathway highlighted by the authors, KEGG_LYSOSOME, is specific to intimal foamy macrophages:

```{r fig.width=5, fig.height=3.5, out.width="50%"}
plotCoregulationProfileReduction(pathways$KEGG_LYSOSOME, 
                               obj,
                               title=sprintf("KEGG_LYSOSOME (pval=%.2g)",
                                             gesecaRes[match("KEGG_LYSOSOME", pathway), pval]),
                               reduction="tsne")
```

## Analysis of spatial transcriptomic data

### Analysis of 10X visium spatial data

Similarly to single cell RNA-seq, GESECA can be used for gene set enrichment analysis of spatial
transcriptomics profiling. As an example we will use glioblastoma 
sample from Ravi et al (https://pubmed.ncbi.nlm.nih.gov/35700707/).

```{r message=FALSE}
library(Seurat)

obj <- readRDS(url("https://alserglab.wustl.edu/files/fgsea/275_T_seurat.rds"))
```


As for scRNA-seq, we apply normalization for 10000 genes and run a do a PCA reduction.

```{r}
obj <- SCTransform(obj, assay = "Spatial", verbose = FALSE, variable.features.n = 10000)

obj <- RunPCA(obj, assay = "SCT", verbose = FALSE,
                rev.pca = TRUE, reduction.name = "pca.rev",
              reduction.key="PCR_", npcs = 50)

E <- obj@reductions$pca.rev@feature.loadings
```

We will use HALLMARK pathways as the gene set collection.

```{r}
library(msigdbr)
pathwaysDF <- msigdbr(species="human", collection="H")
pathways <- split(pathwaysDF$gene_symbol, pathwaysDF$gs_name)
```

Now we can run the analysis (remember, we set `center=FALSE` because we use the 
reduced matrix):

```{r}
set.seed(1)
gesecaRes <- geseca(pathways, E, minSize = 15, maxSize = 500, center = FALSE)

head(gesecaRes, 10)
```

Finally, let us plot spatial expression of the top four pathways:

```{r fig.width=10, fig.height=7, out.width="100%"}

topPathways <- gesecaRes[, pathway] |> head(4)
titles <- sub("HALLMARK_", "", topPathways)

pt.size.factor <- 1.6


# Starting from Seurat version 5.1.0, the scaling method for spatial plots was changed.
# As mentioned here: https://github.com/satijalab/seurat/issues/9049
# This code provides a workaround to adapt to the new scaling behavior.
if (packageVersion("Seurat") >= "5.1.0"){
    sfactors <- ScaleFactors(obj@images$slice1)
    pt.size.factor <- 1.5 * sfactors$fiducial / sfactors$hires
}

ps <- plotCoregulationProfileSpatial(pathways[topPathways], obj,
                                     title=titles, 
                                     pt.size.factor=pt.size.factor)
cowplot::plot_grid(plotlist=ps, ncol=2)
```

<!-- ![](geseca-spatial-top.png){width=100%} -->

Consistent with the Ravi et al, we see a distinct hypoxic region (defined by HALLMARK_HYPOXIA) and a reactive immune region (defined by HALLMARK_INTERFERON_GAMMA_RESPONSE). Further, we can explore behavior of 
HALLMARK_OXIDATIVE_PHOSPHORYLATION pathway to see that oxidative metabolism
is more characteristic to the "normal" tissue region:

```{r fig.width=5, fig.height=3.5, out.width="50%"}
plotCoregulationProfileSpatial(pathways$HALLMARK_OXIDATIVE_PHOSPHORYLATION,
                               obj,
                               pt.size.factor=pt.size.factor,
                               title=sprintf("HALLMARK_OXIDATIVE_PHOSPHORYLATION\n(pval=%.2g)",
                                             gesecaRes[
                                                 match("HALLMARK_OXIDATIVE_PHOSPHORYLATION", pathway),
                                                 pval]))
```


### Analysis of 10X xenium spatial transcriptomics data

GESECA can also be applied to spatial transcriptomics data generated by high-plex in situ technologies with subcellular resolution, such as 10X Genomics' Xenium platform. In this example, we analyze a Human Ovarian Cancer sample profiled using the Xenium 5K panel.

The raw data used in this analysis is publicly available and can be downloaded from the following sources:

- Xenium output bundle: [Download link](https://s3-us-west-2.amazonaws.com/10x.files/samples/xenium/3.0.0/Xenium_Prime_Ovarian_Cancer_FFPE_XRrun/Xenium_Prime_Ovarian_Cancer_FFPE_XRrun_outs.zip)
- Cell annotation file: [Download link](https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_Ovarian_Cancer_FFPE_XRrun/Xenium_Prime_Ovarian_Cancer_FFPE_XRrun_cell_groups.csv)


To prepare the data for GESECA analysis, we carried out the following custom preprocessing steps using Seurat:

```{r eval=FALSE}
fldr <- ""         # Path to downloaded Xenium output
annf_path <- ""    # Path to downloaded cell annotation CSV

# Load the Xenium data as a Seurat object
xobj <- Seurat::LoadXenium(fldr, molecule.coordinates = FALSE)

# Remove assays not needed for downstream analysis
for (nm in names(xobj@assays)[-1]) {
    xobj@assays[[nm]] <- NULL
}

# Add spatial coordinates to metadata
coords <- data.table::as.data.table(xobj@images$fov@boundaries$centroids@coords)
xobj@meta.data <- cbind(xobj@meta.data, coords)

# Integrate external cell annotations
annot <- data.table::fread(annf_path)
xobj <- xobj[, rownames(xobj@meta.data) %in% annot$cell_id]
xobj@meta.data$annotation <- annot[match(rownames(xobj@meta.data), annot$cell_id), ]$group
xobj@meta.data$annotation <- factor(xobj@meta.data$annotation)



# Filter out low-quality cells
xobj <- subset(xobj, subset = nCount_Xenium > 50)


# Optional: Crop the region and subsample the object
# These steps reduce size and complexity for a more compact vignette
# Helps keep the vignette lightweight and quick to render
xobj <- xobj[, xobj$x < 3000 & xobj$y < 4000]
set.seed(1)
xobj <- xobj[, sample.int(ncol(xobj), 40000)]

# Normalize and scale data
xobj <- NormalizeData(xobj, normalization.method = "LogNormalize", scale.factor = 1000, verbose = FALSE)
xobj <- FindVariableFeatures(xobj, nfeatures = 2000, verbose = FALSE)
xobj <- ScaleData(xobj, verbose = FALSE)

# Perform PCA and UMAP dimensionality reduction
xobj <- RunPCA(xobj, verbose = FALSE)
xobj <- RunUMAP(xobj, dims = 1:20)
```

Additionally, before saving the object for use in the vignette, we remove the following components from the Seurat object to reduce its size and keep it tidy:
```{r eval=FALSE}
xobj@reductions$pca <- NULL
xobj@assays$Xenium@layers$scale.data <- NULL
xobj@assays$Xenium@layers$data <- NULL
```


For this tutorial, we directly use the Seurat object that was preprocessed using the steps described above:
```{r}
xobj <- readRDS(url("https://alserglab.wustl.edu/files/fgsea/xenium-human-ovarian-cancer.rds"))

xobj <- NormalizeData(xobj, verbose = FALSE)
xobj <- ScaleData(xobj, verbose = FALSE)
```


The plot below compares the spatial localization of annotated cells (left) with their transcriptional similarity via UMAP (right):

```{r fig.width=10, fig.height=5, out.width="100%"}
p1 <- ImageDimPlot(xobj, group.by = "annotation",
                   dark.background = FALSE, size = 0.5, 
                   flip_xy = TRUE) + 
    theme(legend.position = "none")

p1 <- suppressMessages(p1 + coord_flip() + scale_x_reverse() + theme(aspect.ratio = 1.0))

p2 <- DimPlot(xobj, group.by = "annotation", raster = FALSE, pt.size = 0.5, stroke.size = 0.0) + 
    coord_fixed()

p1 | p2
```

The command `suppressMessages(p1 + coord_flip() + scale_x_reverse() + theme(aspect.ratio = 1.0))` adjusts the plot orientation to match the spatial layout shown in the [Xenium Explorer web viewer](https://www.10xgenomics.com/datasets/xenium-prime-ffpe-human-ovarian-cancer), ensuring consistency between the analysis and the original data presentation.

We will now perform the GESECA analysis in the same manner as previously demonstrated with both scRNA-seq and Visium datasets. For consistency and interpretability, we will once again use the HALLMARK gene sets from the MSigDB collection.

```{r}
xobj <- RunPCA(xobj, verbose = F, rev.pca = TRUE, reduction.name = "pca.rev", 
               reduction.key="PCR_", npcs=30)

E <- xobj@reductions$pca.rev@feature.loadings

gsets <- msigdbr(species="human", collection="H")
gsets <- split(gsets$gene_symbol, gsets$gs_name)

set.seed(1)
gesecaRes <- geseca(gsets, E, minSize = 15, maxSize = 500, center = FALSE, eps = 1e-100)

head(gesecaRes, 10)
```

Next, we visualize the top enriched pathways identified by GESECA using UMAP embeddings. This allows us to assess transcriptional patterns of gene set activity across cells.


```{r fig.width=10, fig.height=7, out.width="100%"}
topPathways <- gesecaRes[, pathway] |> head(6)
titles <- sub("HALLMARK_", "", topPathways)
pvals <- gesecaRes[match(topPathways, pathway), pval]
pvals <- paste("p-value:", formatC(pvals, digits = 1, format = "e"))

titles <- paste(titles, pvals, sep = "\n")

plots <- fgsea::plotCoregulationProfileReduction(
    gsets[topPathways], xobj, 
    reduction = "umap", title = titles,
    raster = TRUE, raster.dpi = c(500, 500),
    pt.size = 2.5
)

plots <- lapply(plots, function(p){
    p + theme(plot.title = element_text(hjust=0), text = element_text(size=10))
})


cowplot::plot_grid(plotlist = plots, ncol = 2)
```

In addition to UMAP plots, you can visualize the spatial expression patterns of the most enriched pathways using the `plotCoregulationProfileImage` function. This enables a detailed view of how pathway activities vary across spatial coordinates:

```{r fig.width=10, fig.height=15, out.width="100%"}
imagePlots <- plotCoregulationProfileImage(
    gsets[topPathways], object = xobj, 
    dark.background = FALSE, 
    title = titles, 
    size=0.8
)

imagePlots <- lapply(imagePlots, function(p){
    suppressMessages(
        p + coord_flip() + scale_x_reverse() + 
            theme(plot.title = element_text(hjust=0), text = element_text(size=10), aspect.ratio = 1.0)
    )
})

cowplot::plot_grid(plotlist = imagePlots, ncol = 2)
```

## Session info

```{r echo=TRUE}
sessionInfo()
```
