Contents

1 Introduction

In this vignette we describe how to generate a SingleCellExperiment object combining observed values and clustering results for a data set from the DuoClustering2018 package, and how the resulting object can be explored and visualized with the iSEE package (Rue-Albrecht et al. 2018).

2 Load the necessary packages

suppressPackageStartupMessages({
  library(SingleCellExperiment)
  library(DuoClustering2018)
  library(dplyr)
  library(tidyr)
})
## snapshotDate(): 2019-04-29

3 Retrieve a data set

The different ways of retrieving a data set from the package are described in the plot_performance vignette. Here, we will load a data set using the shortcut function provided in the package.

dat <- sce_filteredExpr10_Koh()
## snapshotDate(): 2019-04-29
## see ?DuoClustering2018 and browseVignettes('DuoClustering2018') for documentation
## downloading 0 resources
## loading from cache 
##     'EH1501 : 1501'

4 Read a set of clustering results

For this data set, we also load a set of clustering results obtained using different clustering methods.

res <- clustering_summary_filteredExpr10_Koh_v2()
## snapshotDate(): 2019-04-29
## see ?DuoClustering2018 and browseVignettes('DuoClustering2018') for documentation
## downloading 0 resources
## loading from cache 
##     'EH1620 : 1620'

5 Merge data and clustering results

We add the cluster labels for one run and for a set of different imposed number of clusters to the data set.

res <- res %>% dplyr::filter(run == 1 & k %in% c(3, 5, 9)) %>%
  dplyr::group_by(method, k) %>% 
  dplyr::filter(is.na(resolution) | resolution == resolution[1]) %>%
  dplyr::ungroup() %>% 
  tidyr::unite(col = method_k, method, k, sep = "_", remove = TRUE) %>% 
  dplyr::select(cell, method_k, cluster) %>%
  tidyr::spread(key = method_k, value = cluster)

colData(dat) <- DataFrame(
  as.data.frame(colData(dat)) %>%
    dplyr::left_join(res, by = c("Run" = "cell"))
)
head(colData(dat))
## DataFrame with 6 rows and 54 columns
##           Run LibraryName     phenoid libsize.drop feature.drop
##   <character> <character> <character>    <logical>    <logical>
## 1  SRR3952323      H7hESC      H7hESC        FALSE        FALSE
## 2  SRR3952325      H7hESC      H7hESC        FALSE        FALSE
## 3  SRR3952326      H7hESC      H7hESC        FALSE        FALSE
## 4  SRR3952327      H7hESC      H7hESC        FALSE        FALSE
## 5  SRR3952328      H7hESC      H7hESC        FALSE        FALSE
## 6  SRR3952329      H7hESC      H7hESC        FALSE        FALSE
##   total_features log10_total_features     total_counts log10_total_counts
##        <integer>            <numeric>        <numeric>          <numeric>
## 1           4895      3.6898414091375 2248411.34571372   6.35187596127693
## 2           4887      3.6891311972345 2271617.36890415   6.35633537184513
## 3           4888     3.68922003726384 584682.409664363   5.76692077094787
## 4           4879     3.68841982200271 3191809.60023222   6.50403711271802
## 5           4873     3.68788552484871 2190384.61049403   6.34052057774775
## 6           4893     3.68966396501577 2187288.93804626   6.33990635512159
##   pct_counts_top_50_features pct_counts_top_100_features
##                    <numeric>                   <numeric>
## 1           18.2789645082187            25.9753898639458
## 2           24.6725290693842             32.222803367377
## 3           22.7328390182813            30.2059881954046
## 4           20.8673775614106             29.003904032128
## 5           21.2879231261916            29.4236885040328
## 6            20.593115356144            27.7401057678724
##   pct_counts_top_200_features pct_counts_top_500_features is_cell_control
##                     <numeric>                   <numeric>       <logical>
## 1            35.5376157218203             52.410940848381           FALSE
## 2            41.5473580607458            57.9692329081111           FALSE
## 3            39.4313075652416            55.2858170919008           FALSE
## 4            38.7855579579296            56.0208594644678           FALSE
## 5            39.3076832898896            56.6409750805386           FALSE
## 6            36.7818664500694            52.7546829572243           FALSE
##        CIDR_3      CIDR_5      CIDR_9   FlowSOM_3   FlowSOM_5   FlowSOM_9
##   <character> <character> <character> <character> <character> <character>
## 1           1           1           1           2           2           4
## 2           1           1           1           2           2           4
## 3           1           1           1           2           2           4
## 4           1           1           1           2           2           4
## 5           1           1           1           2           2           4
## 6           1           1           1           2           2           4
##       PCAHC_3     PCAHC_5     PCAHC_9 PCAKmeans_3 PCAKmeans_5 PCAKmeans_9
##   <character> <character> <character> <character> <character> <character>
## 1           1           1           1           3           1           4
## 2           1           1           1           3           1           4
## 3           1           1           1           3           1           4
## 4           1           1           1           3           1           4
## 5           1           1           1           3           1           4
## 6           1           1           1           3           1           4
##     RaceID2_3   RaceID2_5   RaceID2_9 RtsneKmeans_3 RtsneKmeans_5
##   <character> <character> <character>   <character>   <character>
## 1           1           1           1             1             1
## 2           2           2           2             1             1
## 3           2           2           2             1             1
## 4           1           1           1             1             1
## 5           1           1           1             1             1
## 6           1           2           2             1             1
##   RtsneKmeans_9      SAFE_3      SAFE_5      SAFE_9       SC3_3       SC3_5
##     <character> <character> <character> <character> <character> <character>
## 1             9           2           1           3           1           3
## 2             9           2           1           5           1           3
## 3             9           2           1           3           1           3
## 4             9           2           1           5           1           3
## 5             9           2           1           5           1           3
## 6             9           2           1           5           1           3
##         SC3_9    SC3svm_3    SC3svm_5    SC3svm_9    Seurat_9     TSCAN_3
##   <character> <character> <character> <character> <character> <character>
## 1           4           3           3           3           5           1
## 2           4           3           3           3           5           1
## 3           4           3           3           3           5           3
## 4           4           3           3           3           5           1
## 5           4           3           3           3           5           2
## 6           4           3           3           3           5           1
##       TSCAN_5     TSCAN_9    ascend_3    ascend_5    ascend_9   monocle_3
##   <character> <character> <character> <character> <character> <character>
## 1           1           1           1          NA          NA           3
## 2           1           2           1          NA          NA           3
## 3           3           2           1          NA          NA           3
## 4           1           1           1          NA          NA           3
## 5           2           2           1          NA          NA           3
## 6           1           1           1          NA          NA           3
##     monocle_5   monocle_9 pcaReduce_3 pcaReduce_5 pcaReduce_9
##   <character> <character> <character> <character> <character>
## 1           3           3           1           5           5
## 2           3           3           1           5           5
## 3           3           3           1           5           5
## 4           3           3           1           5           5
## 5           3           3           1           5           5
## 6           3           3           1           5           5

6 Visualize with iSEE

The resulting SingleCellExperiment can be interactively explored using, e.g., the iSEE package. This can be useful to gain additional understanding of the partitions inferred by the different clustering methods, to visualize these in low-dimensional representations (PCA or t-SNE), and to investigate how well they agree with known or inferred groupings of the cells.

if (require(iSEE)) {
  iSEE(dat)
}

7 Session info

sessionInfo()
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.9-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.9-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] tidyr_0.8.3                 dplyr_0.8.0.1              
##  [3] DuoClustering2018_1.2.0     SingleCellExperiment_1.6.0 
##  [5] SummarizedExperiment_1.14.0 DelayedArray_0.10.0        
##  [7] BiocParallel_1.18.0         matrixStats_0.54.0         
##  [9] Biobase_2.44.0              GenomicRanges_1.36.0       
## [11] GenomeInfoDb_1.20.0         IRanges_2.18.0             
## [13] S4Vectors_0.22.0            BiocGenerics_0.30.0        
## [15] BiocStyle_2.12.0           
## 
## loaded via a namespace (and not attached):
##  [1] viridis_0.5.1                 httr_1.4.0                   
##  [3] bit64_0.9-7                   viridisLite_0.3.0            
##  [5] AnnotationHub_2.16.0          shiny_1.3.2                  
##  [7] assertthat_0.2.1              interactiveDisplayBase_1.22.0
##  [9] BiocManager_1.30.4            BiocFileCache_1.8.0          
## [11] blob_1.1.1                    GenomeInfoDbData_1.2.1       
## [13] yaml_2.2.0                    pillar_1.3.1                 
## [15] RSQLite_2.1.1                 lattice_0.20-38              
## [17] glue_1.3.1                    digest_0.6.18                
## [19] promises_1.0.1                XVector_0.24.0               
## [21] colorspace_1.4-1              htmltools_0.3.6              
## [23] httpuv_1.5.1                  Matrix_1.2-17                
## [25] plyr_1.8.4                    pkgconfig_2.0.2              
## [27] bookdown_0.9                  zlibbioc_1.30.0              
## [29] xtable_1.8-4                  purrr_0.3.2                  
## [31] scales_1.0.0                  later_0.8.0                  
## [33] tibble_2.1.1                  ggplot2_3.1.1                
## [35] lazyeval_0.2.2                mime_0.6                     
## [37] magrittr_1.5                  crayon_1.3.4                 
## [39] mclust_5.4.3                  memoise_1.1.0                
## [41] evaluate_0.13                 ggthemes_4.1.1               
## [43] tools_3.6.0                   stringr_1.4.0                
## [45] munsell_0.5.0                 AnnotationDbi_1.46.0         
## [47] compiler_3.6.0                rlang_0.3.4                  
## [49] grid_3.6.0                    RCurl_1.95-4.12              
## [51] rappdirs_0.3.1                bitops_1.0-6                 
## [53] rmarkdown_1.12                ExperimentHub_1.10.0         
## [55] gtable_0.3.0                  DBI_1.0.0                    
## [57] curl_3.3                      reshape2_1.4.3               
## [59] R6_2.4.0                      gridExtra_2.3                
## [61] knitr_1.22                    bit_1.1-14                   
## [63] stringi_1.4.3                 Rcpp_1.0.1                   
## [65] dbplyr_1.4.0                  tidyselect_0.2.5             
## [67] xfun_0.6

References

Rue-Albrecht, K, F Marini, C Soneson, and ATL Lun. 2018. “iSEE: Interactive SummarizedExperiment Explorer.” F1000Research 7:741.