vignettes/clustSIGNAL.Rmd
clustSIGNAL.Rmd
## [1] "Calculating PCA. Time 23:09:00" -## [1] "clustSIGNAL run started. Time 23:09:01" -## [1] "Initial nonspatial clustering performed. Clusters = 11 Time 23:09:01" -## [1] "Nonspatial subclustering performed. Subclusters = 52 Time 23:09:03" -## [1] "Regions defined. Time 23:09:06" -## [1] "Region domainness calculated. Time 23:09:06" -## [1] "Smoothing performed. NN = 30 Kernel = G Spread = 0.05 Time 23:10:02" -## [1] "Nonspatial clustering performed on smoothed data. Clusters = 14 Time 23:10:03" -## [1] "clustSIGNAL run completed. 23:10:03" -## Time difference of 1.061019 mins
## [1] "Calculating PCA. Time 00:22:28" +## [1] "clustSIGNAL run started. Time 00:22:28" +## [1] "Initial nonspatial clustering performed. Clusters = 11 Time 00:22:29" +## [1] "Nonspatial subclustering performed. Subclusters = 52 Time 00:22:31" +## [1] "Regions defined. Time 00:22:34" +## [1] "Region domainness calculated. Time 00:22:34" +## [1] "Smoothing performed. NN = 30 Kernel = G Spread = 0.05 Time 00:23:29" +## [1] "Nonspatial clustering performed on smoothed data. Clusters = 14 Time 00:23:31" +## [1] "clustSIGNAL run completed. 00:23:31" +## Time difference of 1.049867 mins
This returns a list that can contain a dataframe of cluster names, a matrix of cell labels from each region’s neighbourhood, a final SpatialExperiment object, or a combination of these, depending on the @@ -359,15 +359,15 @@
## [1] "Initial nonspatial clustering performed. Clusters = 11 Time 23:10:13" -## [1] "Nonspatial subclustering performed. Subclusters = 52 Time 23:10:15"
## [1] "Initial nonspatial clustering performed. Clusters = 11 Time 00:23:40" +## [1] "Nonspatial subclustering performed. Subclusters = 52 Time 00:23:43"
outReg <- clustSIGNAL::neighbourDetect(spe, samples = "sample_id", NN = 30, cells = "uniqueID", sort = TRUE)
## [1] "Regions defined. Time 23:10:17"
## [1] "Regions defined. Time 00:23:45"
spe <- entropyMeasure(spe, cells = "uniqueID", outReg$regXclust, threads = 1)
## [1] "Region domainness calculated. Time 23:10:18"
## [1] "Region domainness calculated. Time 00:23:45"
head(spe$entropy)
## [1] 1.30331 0.56083 0.87851 0.97034 0.94808 0.35336
## [1] "Calculating PCA. Time 23:10:18" -## [1] "clustSIGNAL run started. Time 23:10:19" -## [1] "Initial nonspatial clustering performed. Clusters = 13 Time 23:10:22"
## [1] "Nonspatial subclustering performed. Subclusters = 57 Time 23:10:24" -## [1] "Regions defined. Time 23:10:27" -## [1] "Region domainness calculated. Time 23:10:29" -## [1] "Smoothing performed. NN = 30 Kernel = G Spread = 0.05 Time 23:10:50" -## [1] "Nonspatial clustering performed on smoothed data. Clusters = 11 Time 23:10:54" -## [1] "clustSIGNAL run completed. 23:10:54" -## Time difference of 35.37587 secs
## [1] "Calculating PCA. Time 00:23:45" +## [1] "clustSIGNAL run started. Time 00:23:46" +## [1] "Initial nonspatial clustering performed. Clusters = 13 Time 00:23:49"
## [1] "Nonspatial subclustering performed. Subclusters = 57 Time 00:23:51" +## [1] "Regions defined. Time 00:23:54" +## [1] "Region domainness calculated. Time 00:23:56" +## [1] "Smoothing performed. NN = 30 Kernel = G Spread = 0.05 Time 00:24:17" +## [1] "Nonspatial clustering performed on smoothed data. Clusters = 11 Time 00:24:20" +## [1] "clustSIGNAL run completed. 00:24:20" +## Time difference of 35.06137 secs
spe2 <- res_hyp$spe_final spe2
Panwar P, Guo B, Zhao H, Hicks S, Ghazanfar S (2024). clustSIGNAL: clustSIGNAL: a spatial clustering method. -R package version 0.99.1, https://sydneybiox.github.io/clustSIGNAL/. +R package version 0.99.2, https://sydneybiox.github.io/clustSIGNAL/.
@Manual{, title = {clustSIGNAL: clustSIGNAL: a spatial clustering method}, author = {Pratibha Panwar and Boyi Guo and Haowen Zhao and Stephanie Hicks and Shila Ghazanfar}, year = {2024}, - note = {R package version 0.99.1}, + note = {R package version 0.99.2}, url = {https://sydneybiox.github.io/clustSIGNAL/}, }