+
+
+
+
+
+Using MOJITOO in R for Matrix input
+Mingbo +Cheng
+ +October 23, 2024
+ + +Matrix_integration.Rmd
+
+1. download data +
+## WARNING: cannot verify costalab.ukaachen.de's certificate, issued by ‘CN=GEANT OV RSA CA 4,O=GEANT Vereniging,C=NL’:
+## Unable to locally verify the issuer's authority.
+## 2024-10-23 12:32:07 URL:https://costalab.ukaachen.de/open_data/MOJITOO/ATAC_LSI.Rds [1380864/1380864] -> "ATAC_LSI.Rds" [1]
+## WARNING: cannot verify costalab.ukaachen.de's certificate, issued by ‘CN=GEANT OV RSA CA 4,O=GEANT Vereniging,C=NL’:
+## Unable to locally verify the issuer's authority.
+## 2024-10-23 12:32:08 URL:https://costalab.ukaachen.de/open_data/MOJITOO/RNA_PCA.Rds [1390391/1390391] -> "RNA_PCA.Rds" [1]
+
+
+
+2. library +
+
+library(MOJITOO)
+
+
+
+3. LOADING DATA +
+ +## PC_1 PC_2 PC_3 PC_4 PC_5
+## ACCTTCCAGGAACGCG-1 -18.722372 3.2061442 -4.427158 -1.6254263 -10.133467
+## GGTTCTTGTCCTTAGT-1 -14.447415 0.6859972 5.093509 7.8732573 21.056898
+## CGTATTGCATTCAGCA-1 9.753255 2.4812830 -4.249865 -3.2154207 1.495905
+## TGAGGCACAACAGGTG-1 -17.249908 1.8702171 -2.040451 0.4033981 -1.186289
+## TCACGGATCTCACAAA-1 6.555031 -14.9040450 1.280343 0.5568495 -2.309631
+
+(ATAC_LSI[1:5, 1:5])
## LSI_1 LSI_2 LSI_3 LSI_4 LSI_5
+## ACCTTCCAGGAACGCG-1 -0.3456660 -1.2187188 -0.29848099 0.07280032 -0.16058723
+## GGTTCTTGTCCTTAGT-1 -0.9354829 -1.6351802 0.01148662 0.04542933 -0.01966307
+## CGTATTGCATTCAGCA-1 0.0485317 0.8786845 -0.40229951 0.88748465 0.46213190
+## TGAGGCACAACAGGTG-1 -0.7041392 -1.2302514 -0.09467401 0.14793960 0.11523086
+## TCACGGATCTCACAAA-1 -0.4350341 0.2969706 2.61745329 -0.28567776 0.47715209
+
+message("dims of pca & lsi: ", nrow(RNA_PCA), " ", ncol(RNA_PCA), ", ",
+ nrow(ATAC_LSI), " ", ncol(ATAC_LSI))
## dims of pca & lsi: 3536 50, 3536 50
+
+
+
+
+4. RUN MOJITOO +
+
+MOJITOO_DM <- mojitoo_Matrix(
+ reduction_matrix.list= list(RNA_PCA, ATAC_LSI),
+ dims.list = list(1:50, 2:50) ## exclude 1st dimension of LSI
+)
## processing 1
+## adding 2
+## 1 round cc 44
+
+MOJITOO_DM[1:5, 1:5]
## mojitoo1 mojitoo2 mojitoo3 mojitoo4 mojitoo5
+## ACCTTCCAGGAACGCG-1 0.3041858 2.62861275 -0.6237414 0.5587585 -2.6407216
+## GGTTCTTGTCCTTAGT-1 0.7631513 3.59702871 -0.4402510 -0.2070474 10.6965888
+## CGTATTGCATTCAGCA-1 0.2236081 -2.02918067 -0.7249151 1.5748186 0.6869435
+## TGAGGCACAACAGGTG-1 0.2447969 2.87887439 -0.5511696 0.2130495 -0.3620080
+## TCACGGATCTCACAAA-1 -3.2072954 -0.08991125 3.4165403 -0.1093769 -0.2516832
+
+## dims of MOJITOO_DM: 3536 44
+
+
+
+ SessionInfo +
+
+sessionInfo()
## R version 4.1.0 (2021-05-18)
+## Platform: x86_64-conda-linux-gnu (64-bit)
+## Running under: Rocky Linux 8.10 (Green Obsidian)
+##
+## Matrix products: default
+## BLAS/LAPACK: /data/sz753404/miniconda3/envs/schema/lib/libopenblasp-r0.3.21.so
+##
+## locale:
+## [1] LC_CTYPE=en_US.utf-8 LC_NUMERIC=C
+## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.utf-8
+## [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.utf-8
+## [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
+## [9] LC_ADDRESS=C LC_TELEPHONE=C
+## [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
+##
+## attached base packages:
+## [1] stats graphics grDevices utils datasets methods base
+##
+## other attached packages:
+## [1] MOJITOO_1.0
+##
+## loaded via a namespace (and not attached):
+## [1] rappdirs_0.3.3 rtracklayer_1.52.1
+## [3] scattermore_0.8 SeuratObject_4.1.3
+## [5] ragg_1.3.3 tidyr_1.2.1
+## [7] ggplot2_3.4.1 bit64_4.0.5
+## [9] knitr_1.42 irlba_2.3.5.1
+## [11] DelayedArray_0.18.0 data.table_1.14.8
+## [13] rpart_4.1.19 KEGGREST_1.34.0
+## [15] RCurl_1.98-1.10 AnnotationFilter_1.16.0
+## [17] doParallel_1.0.16 generics_0.1.3
+## [19] BiocGenerics_0.40.0 GenomicFeatures_1.44.2
+## [21] cowplot_1.1.1 RSQLite_2.3.0
+## [23] RANN_2.6.1 future_1.28.0
+## [25] bit_4.0.5 spatstat.data_3.0-0
+## [27] xml2_1.3.3 httpuv_1.6.5
+## [29] SummarizedExperiment_1.22.0 assertthat_0.2.1
+## [31] xfun_0.37 hms_1.1.2
+## [33] jquerylib_0.1.4 evaluate_0.20
+## [35] promises_1.2.0.1 fansi_1.0.4
+## [37] restfulr_0.0.13 progress_1.2.2
+## [39] dbplyr_2.3.1 igraph_1.4.1
+## [41] DBI_1.1.3 htmlwidgets_1.6.1
+## [43] spatstat.geom_3.0-3 stats4_4.1.0
+## [45] purrr_1.0.1 ellipsis_0.3.2
+## [47] ks_1.13.3 dplyr_1.1.0
+## [49] backports_1.4.1 biomaRt_2.48.3
+## [51] deldir_1.0-6 MatrixGenerics_1.4.3
+## [53] vctrs_0.5.2 Biobase_2.54.0
+## [55] here_1.0.1 ensembldb_2.16.4
+## [57] ROCR_1.0-11 abind_1.4-5
+## [59] cachem_1.0.7 Gviz_1.36.2
+## [61] BSgenome_1.60.0 progressr_0.10.1
+## [63] checkmate_2.1.0 sctransform_0.3.5
+## [65] GenomicAlignments_1.28.0 prettyunits_1.1.1
+## [67] mclust_5.4.9 goftest_1.2-3
+## [69] cluster_2.1.4 lazyeval_0.2.2
+## [71] crayon_1.5.2 spatstat.explore_3.0-5
+## [73] pkgconfig_2.0.3 GenomeInfoDb_1.30.1
+## [75] nlme_3.1-160 ProtGenerics_1.26.0
+## [77] nnet_7.3-18 rlang_1.0.6
+## [79] globals_0.16.1 lifecycle_1.0.3
+## [81] miniUI_0.1.1.1 filelock_1.0.2
+## [83] BiocFileCache_2.0.0 dichromat_2.0-0.1
+## [85] rprojroot_2.0.3 polyclip_1.10-4
+## [87] matrixStats_0.62.0 lmtest_0.9-40
+## [89] Matrix_1.5-3 Rhdf5lib_1.16.0
+## [91] zoo_1.8-10 base64enc_0.1-3
+## [93] ggridges_0.5.3 GlobalOptions_0.1.2
+## [95] png_0.1-8 viridisLite_0.4.1
+## [97] rjson_0.2.20 bitops_1.0-7
+## [99] KernSmooth_2.23-20 rhdf5filters_1.4.0
+## [101] Biostrings_2.62.0 blob_1.2.3
+## [103] shape_1.4.6 stringr_1.5.0
+## [105] parallelly_1.32.1 spatstat.random_3.0-1
+## [107] jpeg_0.1-9 S4Vectors_0.32.4
+## [109] scales_1.2.1 memoise_2.0.1
+## [111] magrittr_2.0.3 plyr_1.8.8
+## [113] ica_1.0-3 zlibbioc_1.40.0
+## [115] hdrcde_3.4 compiler_4.1.0
+## [117] BiocIO_1.2.0 RColorBrewer_1.1-3
+## [119] clue_0.3-60 fitdistrplus_1.1-8
+## [121] Rsamtools_2.8.0 cli_3.6.0
+## [123] XVector_0.34.0 listenv_0.8.0
+## [125] patchwork_1.1.2 pbapply_1.7-0
+## [127] htmlTable_2.3.0 Formula_1.2-4
+## [129] MASS_7.3-58.1 tidyselect_1.2.0
+## [131] stringi_1.7.12 textshaping_0.3.6
+## [133] yaml_2.3.7 latticeExtra_0.6-29
+## [135] ggrepel_0.9.3 grid_4.1.0
+## [137] sass_0.4.5 VariantAnnotation_1.38.0
+## [139] tools_4.1.0 future.apply_1.9.0
+## [141] parallel_4.1.0 circlize_0.4.13
+## [143] rstudioapi_0.14 foreach_1.5.2
+## [145] foreign_0.8-84 gridExtra_2.3
+## [147] Rtsne_0.16 digest_0.6.31
+## [149] pracma_2.3.8 shiny_1.7.2
+## [151] Rcpp_1.0.10 GenomicRanges_1.44.0
+## [153] later_1.3.0 RcppAnnoy_0.0.19
+## [155] fda_5.5.1 httr_1.4.5
+## [157] AnnotationDbi_1.56.2 biovizBase_1.40.0
+## [159] ComplexHeatmap_2.11.1 colorspace_2.1-0
+## [161] XML_3.99-0.13 fs_1.6.1
+## [163] tensor_1.5 rainbow_3.6
+## [165] reticulate_1.25 IRanges_2.28.0
+## [167] splines_4.1.0 uwot_0.1.14
+## [169] spatstat.utils_3.1-0 pkgdown_2.0.3
+## [171] sp_1.5-1 ArchR_1.0.1
+## [173] plotly_4.10.1 systemfonts_1.0.4
+## [175] xtable_1.8-4 jsonlite_1.8.4
+## [177] fds_1.8 corpcor_1.6.10
+## [179] R6_2.5.1 Hmisc_5.0-1
+## [181] ramify_0.3.3 pillar_1.8.1
+## [183] htmltools_0.5.4 mime_0.12
+## [185] glue_1.6.2 fastmap_1.1.1
+## [187] BiocParallel_1.28.3 deSolve_1.32
+## [189] codetools_0.2-19 pcaPP_2.0-1
+## [191] mvtnorm_1.1-3 utf8_1.2.3
+## [193] lattice_0.20-45 bslib_0.4.2
+## [195] spatstat.sparse_3.0-0 tibble_3.2.0
+## [197] curl_5.0.0 leiden_0.4.2
+## [199] survival_3.5-5 rmarkdown_2.20
+## [201] desc_1.4.2 munsell_0.5.0
+## [203] GetoptLong_1.0.5 rhdf5_2.36.0
+## [205] GenomeInfoDbData_1.2.7 iterators_1.0.14
+## [207] reshape2_1.4.4 gtable_0.3.1
+## [209] Seurat_4.3.0
+