Author: Edward Zhao, Matt Stone, Xing Ren, and Raphael Gottardo

# BayesSpace

    library(SingleCellExperiment)
    library(ggplot2)
    library(BayesSpace)

## Preparing your experiment for BayesSpace

### Loading data

BayesSpace supports three ways of loading a `SingleCellExperiment` for analysis.

Visium datasets processed with Space Ranger can be loaded directly via the `readVisium()` function. This function takes only the path to the Space Ranger output directory (containing the `spatial/` and `filtered_feature_bc_matrix/` subdirectories) and returns a `SingleCellExperiment`.

    sce <- readVisium("path/to/spaceranger/outs/")

Second, all datasets analyzed for the BayesSpace manuscript are readily accessible via the `getRDS()` function. This function takes two arguments - the name of the dataset, and the name of the sample in the dataset.

    melanoma <- getRDS(dataset="2018_thrane_melanoma", sample="ST_mel1_rep2")

Finally, `SingleCellExperiment` objects can be constructed manually from a counts matrix and tables of row and column data. BayesSpace only requires that spot array coordinates be provided as columns named `array_row` and `array_col` in `colData`. (Note that enhancement of Visium datasets additionally requires the pixel coordinates of each spot in the tissue image, but in this case the dataset should be loaded with `readVisium()`, which loads these data automatically.)

    library(Matrix)

    rowData <- read.csv("path/to/rowData.csv", stringsAsFactors=FALSE)
    colData <- read.csv("path/to/colData.csv", stringsAsFactors=FALSE, row.names=1)
    counts <- read.csv("path/to/counts.csv.gz",
                       row.names=1, check.names=F, stringsAsFactors=FALSE))

    sce <- SingleCellExperiment(assays=list(counts=as(counts, "dgCMatrix")),
                                rowData=rowData,
                                colData=colData)

We’ll continue with the melanoma sample from the 2018 Spatial Transcriptomics paper for the remaining examples in this vignette.

### Pre-processing data

BayesSpace requires minimal data pre-processing, but we provide a helper function to automate it.

`spatialPreprocess()` log-normalizes the count matrix and performs PCA on the top `n.HVGs` highly variable genes, keeping the top `n.PCs` principal components. Additionally, the spatial sequencing platform is added as metadata in the `SingleCellExperiment` for downstream analyses. If you do not wish to rerun PCA, running `spatialPreprocess()` with the flag `skip.PCA=TRUE` will only add the metadata BayesSpace requires.

    set.seed(102)
    melanoma <- spatialPreprocess(melanoma, platform="ST",
                                  n.PCs=7, n.HVGs=2000, log.normalize=TRUE)

## Clustering

### Selecting the number of clusters

We can use the `qTune()` and `qPlot()` functions to help choose `q`, the number of clusters to use in our analysis.

- `qTune()` runs the BayesSpace clustering algorithm for multiple specified values of `q` (by default, 3 through 7) and computes their average pseudo-log-likelihood. It accepts any arguments to `spatialCluster()`.
- `qPlot()` plots the pseudo-log-likelihood as a function of `q`; we suggest choosing a `q` around the elbow of this plot.

    melanoma <- qTune(melanoma, qs=seq(2, 10), platform="ST", d=7, cores=2)
    qPlot(melanoma)

### Clustering with BayesSpace

The `spatialCluster()` function clusters the spots, and adds the predicted cluster labels to the `SingleCellExperiment`. Typically, as we did for the analyses in the paper, we suggest running with at least 10,000 iterations (`nrep=10000`), but we use 2,000 iteration in this demonstration for the sake of runtime. (Note that a random seed must be set in order for the results to be reproducible.)

    set.seed(149)
    melanoma <- spatialCluster(melanoma, q=4, platform="ST", d=7,
                               init.method="mclust", model="t", gamma=2,
                               nrep=2000, burn.in=100,
                               save.chain=TRUE)

Both the mclust initialization (`cluster.init`) and the BayesSpace cluster assignments (`spatial.cluster`) are now available in the SingleCellExperiment’s `colData`.

    head(colData(melanoma))
    #> DataFrame with 6 rows and 9 columns
    #>          barcode in_tissue array_row array_col sizeFactor  spot.idx
    #>      <character> <logical> <numeric> <numeric>  <numeric> <integer>
    #> 7x15        7x15      TRUE         7        15   0.795588         1
    #> 7x16        7x16      TRUE         7        16   0.307304         2
    #> 7x17        7x17      TRUE         7        17   0.331247         3
    #> 7x18        7x18      TRUE         7        18   0.420747         4
    #> 8x13        8x13      TRUE         8        13   0.255453         5
    #> 8x14        8x14      TRUE         8        14   1.473439         6
    #>      spot.neighbors cluster.init spatial.cluster
    #>         <character>    <numeric>       <numeric>
    #> 7x15            2,7            1               1
    #> 7x16          1,3,8            1               1
    #> 7x17          2,4,9            2               2
    #> 7x18           3,10            3               2
    #> 8x13           6,12            1               1
    #> 8x14         5,7,13            1               1

### Visualizing spatial clusters

We can plot the cluster assignments over the spatial locations of the spots with `clusterPlot()`.

    clusterPlot(melanoma)

As `clusterPlot()` returns a `ggplot` object, it can be customized by composing with familiar `ggplot2` functions. Additionally, the argument `palette` sets the colors used for each cluster, and `clusterPlot()` takes additional arguments to `geom_polygon()` such as `size` or `color` to control the aesthetics of the spot borders.

    clusterPlot(melanoma, palette=c("purple", "red", "blue", "yellow"), color="black") +
      theme_bw() +
      xlab("Column") +
      ylab("Row") +
      labs(fill="BayesSpace\ncluster", title="Spatial clustering of ST_mel1_rep2")

## Enhanced resolution

### Clustering at enhanced resolution

The `spatialEnhance()` function will enhance the resolution of the principal components, and add these PCs as well as predicted cluster labels at subspot resolution to a new `SingleCellExperiment`. As with our demonstration of `spatialCluster()` above, we are using fewer iterations for the purpose of this example (`nrep=2000`) than we recommend in practice (`nrep=100000` or greater).

Note that the `jitter_scale` parameter should be tuned so that proposals for updating subspot-level expression are accepted around 30% of the time. This can be evaluated using `mcmcChain(melanoma.enhanced, "Ychange")`, where the chain should stabilize to 0.25-0.40. Typically 1000-2500 iterations are sufficient to evaluate if `jitter_scale` should be increased if acceptance is too high or decreased if acceptance is too low.

We have implemented another way to avoid manually tuning `jitter_scale`, which uses adaptive MCMC. To use this feature, simply set `jitter.scale=0`. BayesSpace will automatically tune this parameter to achieve the best acceptance rate. Note that such tuning by default only happens in the burn-in phase.

After tuning, proceed to a full run of `spatialEnhance` with more iterations.

    melanoma.enhanced <- spatialEnhance(melanoma, q=4, platform="ST", d=7,
                                        model="t", gamma=2,
                                        jitter.prior=0.3, jitter.scale=0,
                                        nrep=2000, burn.in=100,
                                        save.chain=TRUE, cores=2)

The enhanced `SingleCellExperiment` includes an index to the parent spot in the original `sce` (`spot.idx`), along with an index to the subspot. It adds the offsets to the original spot coordinates, and provides the enhanced cluster label (`spatial.cluster`).

    head(colData(melanoma.enhanced))
    #> DataFrame with 6 rows and 9 columns
    #>              spot.idx spot.neighbors subspot.idx subspot.neighbors  spot.row
    #>             <numeric>    <character>   <integer>       <character> <numeric>
    #> subspot_1.1         1            2,7           1           294,880         7
    #> subspot_2.1         2          1,3,8           1       295,587,881         7
    #> subspot_3.1         3          2,4,9           1       296,588,882         7
    #> subspot_4.1         4           3,10           1       297,589,883         7
    #> subspot_5.1         5           6,12           1           298,884         8
    #> subspot_6.1         6         5,7,13           1       299,591,885         8
    #>              spot.col array_row array_col spatial.cluster
    #>             <numeric> <numeric> <numeric>       <numeric>
    #> subspot_1.1        15   6.66667   14.6667               1
    #> subspot_2.1        16   6.66667   15.6667               1
    #> subspot_3.1        17   6.66667   16.6667               2
    #> subspot_4.1        18   6.66667   17.6667               2
    #> subspot_5.1        13   7.66667   12.6667               1
    #> subspot_6.1        14   7.66667   13.6667               1

We can plot the enhanced cluster assignments as above.

    clusterPlot(melanoma.enhanced)

### Enhancing the resolution of gene expression

BayesSpace operates on the principal components of the gene expression matrix, and `spatialEnhance()` therefore computes enhanced resolution PC vectors. Enhanced gene expression is not computed directly, and is instead imputed using a regression algorithm. For each gene, a model using the PC vectors of each spot is trained to predict the spot-level gene expression, and the fitted model is used to predict subspot expression from the subspot PCs.

Gene expression enhancement is implemented in the `enhanceFeatures()` function. BayesSpace predicts expression with `xgboost` by default, but linear and Dirichlet regression are also available via the `model` argument. When using `xgboost`, we suggest automatically tuning the `nrounds` parameter by setting it to 0, although this comes at the cost of increased runtime (~4x slower than a pre-specified `nrounds` in practice).

`enhanceFeatures()` can be used to impute subspot-level expression for all genes, or for a subset of genes of interest. Here, we’ll demonstrate by enhancing the expression of four marker genes: PMEL (ENSG00000185664, melanoma), CD2 (ENSG00000116824, T-cells), CD19 (ENSG00000177455, B-cells), and COL1A1 (ENSG00000108821, fibroblasts).

    markers <- c("ENSG00000185664", "ENSG00000116824", "ENSG00000177455", "ENSG00000108821")
    melanoma.enhanced <- enhanceFeatures(melanoma.enhanced, melanoma,
                                         feature_names=markers,
                                         nrounds=0)

By default, log-normalized expression (`logcounts(sce)`) is imputed, although other assays or arbitrary feature matrices can be specified.

    logcounts(melanoma.enhanced)[markers, 1:5]
    #>                 subspot_1.1 subspot_2.1 subspot_3.1 subspot_4.1 subspot_5.1
    #> ENSG00000185664   2.6861687   2.3220320   2.4178734   2.4517002   2.3524215
    #> ENSG00000116824   0.3534248   0.3267934   0.2882063   0.2882063   0.3267934
    #> ENSG00000177455   0.6186710   0.3533678   0.4263284   0.4263284   0.4263284
    #> ENSG00000108821   0.0000000   1.1709466   1.2610886   1.1541052   1.0145169

Diagnostic measures from each predictive model, such as `rmse` when using `xgboost`, are added to the `rowData` of the enhanced dataset.

    rowData(melanoma.enhanced)[markers, ]
    #> DataFrame with 4 rows and 4 columns
    #>                         gene_id   gene_name    is.HVG enhanceFeatures.rmse
    #>                     <character> <character> <logical>            <numeric>
    #> ENSG00000185664 ENSG00000185664        PMEL      TRUE             0.902616
    #> ENSG00000116824 ENSG00000116824         CD2      TRUE             0.649966
    #> ENSG00000177455 ENSG00000177455        CD19      TRUE             0.701261
    #> ENSG00000108821 ENSG00000108821      COL1A1      TRUE             0.613523

### Visualizing enhanced gene expression

Spatial gene expression is visualized with `featurePlot()`.

    featurePlot(melanoma.enhanced, "ENSG00000185664")

Here, we compare the spatial expression of the imputed marker genes.

    enhanced.plots <- purrr::map(markers, function(x) featurePlot(melanoma.enhanced, x))
    patchwork::wrap_plots(enhanced.plots, ncol=2)

And we can compare to the spot-level expression.

    spot.plots <- purrr::map(markers, function(x) featurePlot(melanoma, x))
    patchwork::wrap_plots(c(enhanced.plots, spot.plots), ncol=4)

## Accessing Markov chains

If `save.chain` is set to `TRUE` in either `spatialCluster()` or `spatialEnhance()`, the chain associated with the respective MCMC run is preserved to disk as an HDF5 file. The path to this file is stored in the SingleCellExperiment’s metadata at `metadata(sce)$h5.chain`, and can be read directly using `mcmcChain()`.

The chain is provided as a `coda::mcmc` object, which can be analyzed with TidyBayes or as a matrix. The object has one row per iteration, with the values of the parameters concatenated across the row. Columns are named with the parameter name and index (if any).

    chain <- mcmcChain(melanoma)
    chain[1:5, 1:5]
    #>      lambda[1,1] lambda[1,2] lambda[1,3]  lambda[1,4] lambda[1,5]
    #> [1,]   0.0100000  0.00000000  0.00000000 0.000000e+00  0.00000000
    #> [2,]   0.1836711  0.01019059  0.08664012 3.994578e-02 -0.02443957
    #> [3,]   0.1790958 -0.04576098  0.07102969 8.286855e-05 -0.10919746
    #> [4,]   0.1730928 -0.02089801  0.08429716 2.803978e-02 -0.10322589
    #> [5,]   0.1923552 -0.02112783  0.07563260 2.088451e-02 -0.04688843

To remove the HDF5 file from disk and remove its path from the metadata, use `removeChain()`.