A clustering method for spatially-resolved cell-type classification of spatial transcriptomics data. The tool generates and uses an adaptively smoothed, spatially informed gene expression data for clustering.
Usage
clustSIGNAL(
spe,
samples,
dimRed = "None",
batch = FALSE,
batch_by = "None",
NN = 30,
kernel = "G",
spread = 0.3,
sort = TRUE,
threads = 1,
outputs = "c",
clustParams = list(clust_c = 0, subclust_c = 0, iter.max = 30, k = 10, cluster.fun =
"louvain")
)Arguments
- spe
a SpatialExperiment object containing spatial coordinates in 'spatialCoords' matrix and normalised gene expression in 'logcounts' assay.
- samples
a character indicating name of colData(spe) column containing sample names.
- dimRed
a character indicating the name of the reduced dimensions to use from the SpatialExperiment object (i.e., from reducedDimNames(spe)). Default value is 'None'.
- batch
a logical parameter for whether to perform batch correction. Default value is FALSE.
- batch_by
a character indicating name of colData(spe) column containing the batch names. Default value is 'None'.
- NN
an integer for the number of neighbouring cells the function should consider. The value must be greater than or equal to 1. Default value is 30.
- kernel
a character for type of distribution to be used. The two valid values are "G" or "E" for Gaussian and exponential distributions, respectively. Default value is "G".
- spread
a numeric value for distribution spread, represented by standard deviation for Gaussian distribution and rate for exponential distribution. Default value is 0.3 for Gaussian distribution. The recommended value is 5 for exponential distribution.
- sort
a logical parameter for whether to sort the neighbourhood by initial clusters. Default value is TRUE.
- threads
a numeric value for the number of CPU cores to be used for the analysis. Default value set to 1.
- outputs
a character for the type of output to return to the user. "c" for data frame of cell IDs and their respective ClustSIGNAL cluster labels, "n" for ClustSIGNAL cluster dataframe plus neighbourhood matrix, "s" for ClustSIGNAL cluster dataframe plus final SpatialExperiment object, or "a" for all 3 outputs.
- clustParams
a list of parameters for TwoStepParam clustering methods: clust_c is the number of centers to use for clustering with KmeansParam. By default set to 0, in which case the method uses either 5000 centers or 1/5th of the total cells in the data as the number of centers, whichever is lower. subclust_c is the number of centers to use for sub-clustering the initial clusters with KmeansParam. The default value is 0, in which case the method uses either 1 center or half of the total cells in the initial cluster as the number of centers, whichever is higher. iter.max is the maximum number of iterations to perform during clustering and sub-clustering with KmeansParam. Default value is 30. k is a numeric value indicating the k-value used for clustering and sub-clustering with NNGraphParam. Default value is 10. cluster.fun is a character indicating the graph clustering method used with NNGraphParam. By default, the Louvain method is used.
Value
a list of outputs depending on the type of outputs specified in the main function call.
1. clusters: a data frame of cell names and their ClustSIGNAL cluster classification.
2. neighbours: a character matrix containing cells IDs of each cell's NN neighbours.
3. spe_final: a SpatialExperiment object containing the original spe object data plus initial cluster and subcluster labels, entropy values, smoothed gene expression, and ClustSIGNAL cluster labels.
Examples
data(ClustSignal_example)
names(colData(spe))
#> [1] "uniqueID" "sample_id" "entropy" "initCluster"
#> [5] "initSubcluster"
# identify the column name with sample labels
samples = "sample_id"
res_list <- clustSIGNAL(spe, samples, outputs = "c")
#> [1] "Calculating PCA. Time 08:51:40"
#> [1] "ClustSIGNAL run started. Time 08:51:40"
#> [1] "Initial nonspatial clustering performed. Clusters = 3 Time 08:51:40"
#> [1] "Nonspatial subclustering performed. Subclusters = 10 Time 08:51:41"
#> [1] "Regions defined. Time 08:51:42"
#> [1] "Region heterogeneity calculated. Time 08:51:42"
#> [1] "Smoothing performed. NN = 30 Kernel = G Spread = 0.3 Time 08:51:42"
#> [1] "Nonspatial clustering performed on smoothed data. Clusters = 7 Time 08:51:42"
#> [1] "ClustSIGNAL run completed. 08:51:42"
#> Time difference of 2.285319 secs