## [1] "Calculating PCA. Time 00:32:08" -## [1] "clustSIGNAL run started. Time 00:32:09" -## [1] "Initial nonspatial clustering performed. Clusters = 11 Time 00:32:09" -## [1] "Nonspatial subclustering performed. Subclusters = 50 Time 00:32:12" -## [1] "Regions defined. Time 00:32:14" -## [1] "Region domainness calculated. Time 00:32:14" -## [1] "Smoothing performed. NN = 30 Kernel = G Spread = 0.05 Time 00:32:51" -## [1] "Nonspatial clustering performed on smoothed data. Clusters = 16 Time 00:32:53" -## [1] "clustSIGNAL run completed. 00:32:53" -## Time difference of 45.32507 secs
## [1] "Calculating PCA. Time 01:11:53" +## [1] "clustSIGNAL run started. Time 01:11:54" +## [1] "Initial nonspatial clustering performed. Clusters = 11 Time 01:11:55" +## [1] "Nonspatial subclustering performed. Subclusters = 50 Time 01:11:57" +## [1] "Regions defined. Time 01:11:59" +## [1] "Region domainness calculated. Time 01:12:00" +## [1] "Smoothing performed. NN = 30 Kernel = G Spread = 0.05 Time 01:12:33" +## [1] "Nonspatial clustering performed on smoothed data. Clusters = 16 Time 01:12:35" +## [1] "clustSIGNAL run completed. 01:12:35" +## Time difference of 41.1917 secs
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 @@ -363,15 +363,15 @@
## [1] "Initial nonspatial clustering performed. Clusters = 11 Time 00:33:02" -## [1] "Nonspatial subclustering performed. Subclusters = 50 Time 00:33:05"
## [1] "Initial nonspatial clustering performed. Clusters = 11 Time 01:12:44" +## [1] "Nonspatial subclustering performed. Subclusters = 50 Time 01:12:46"
outReg <- clustSIGNAL::neighbourDetect(spe, samples = "sample_id", NN = 30, cells = "uniqueID", sort = TRUE)
## [1] "Regions defined. Time 00:33:07"
## [1] "Regions defined. Time 01:12:48"
spe <- entropyMeasure(spe, cells = "uniqueID", outReg$regXclust, threads = 1)
## [1] "Region domainness calculated. Time 00:33:08"
## [1] "Region domainness calculated. Time 01:12:48"
head(spe$entropy)
## [1] 1.03701 0.42003 0.62749 0.76651 0.56651 0.21084
## [1] "Calculating PCA. Time 00:33:08" -## [1] "clustSIGNAL run started. Time 00:33:08" -## [1] "Initial nonspatial clustering performed. Clusters = 11 Time 00:33:09"
## [1] "Nonspatial subclustering performed. Subclusters = 52 Time 00:33:11" -## [1] "Regions defined. Time 00:33:14" -## [1] "Region domainness calculated. Time 00:33:16" -## [1] "Smoothing performed. NN = 30 Kernel = G Spread = 0.05 Time 00:33:33" -## [1] "Nonspatial clustering performed on smoothed data. Clusters = 11 Time 00:33:35" -## [1] "clustSIGNAL run completed. 00:33:35" -## Time difference of 26.87564 secs
## [1] "Calculating PCA. Time 01:12:49" +## [1] "clustSIGNAL run started. Time 01:12:49" +## [1] "Initial nonspatial clustering performed. Clusters = 11 Time 01:12:50"
## [1] "Nonspatial subclustering performed. Subclusters = 52 Time 01:12:52" +## [1] "Regions defined. Time 01:12:54" +## [1] "Region domainness calculated. Time 01:12:56" +## [1] "Smoothing performed. NN = 30 Kernel = G Spread = 0.05 Time 01:13:11" +## [1] "Nonspatial clustering performed on smoothed data. Clusters = 11 Time 01:13:13" +## [1] "clustSIGNAL run completed. 01:13:13" +## Time difference of 23.97924 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 0.99.4, https://sydneybiox.github.io/clustSIGNAL/. +R package version 0.99.5, 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 0.99.4}, + note = {R package version 0.99.5}, url = {https://sydneybiox.github.io/clustSIGNAL/}, }
NEWS.md