diff --git a/DESCRIPTION b/DESCRIPTION index 05867f1..9dfba9d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: icWGCNA Title: Iterative Correcting Weighted Gene Co-expression Network Analysis -Version: 0.4.0 +Version: 0.4.1 Authors@R: c( person("Mike", "Mason", , "mike.mason@bms.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-5652-7739")), @@ -35,7 +35,7 @@ Suggests: foreach, ggplot2, mockery, - msigdbr, + msigdbdf (>= 24.1.0), parallel, purrr, R.utils, @@ -52,9 +52,11 @@ Suggests: LinkingTo: Rcpp, RcppEigen -Remotes: dviraran/xCell +Remotes: + dviraran/xCell, + igordot/msigdbdf Config/testthat/edition: 3 Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Config/testthat/parallel: true diff --git a/NEWS.md b/NEWS.md index 4722e6e..1a95c40 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# icWGCNA 0.4.1 + +- Fixed bug in `map_eigengenes_on_seurat()` when cutoff method is "value" +- Updated MSigDB data for `compute_MSigDB_enrichment()` + # icWGCNA 0.4.0 ### New Features diff --git a/R/downstream.R b/R/downstream.R index 3060ddd..3deee4a 100644 --- a/R/downstream.R +++ b/R/downstream.R @@ -292,7 +292,7 @@ compute_MSigDB_enrichment <- function(membership_matrix, memb_cut = .65, cats = c("H", "C3", "C6", "C7", "C8"), p_cut = 0.001) { - needed_packages <- c('msigdbr', 'foreach', 'tidyr') + needed_packages <- c('msigdbdf', 'foreach', 'tidyr') missing_packages <- !vapply(needed_packages, FUN = requireNamespace, quietly = TRUE, FUN.VALUE = logical(1)) @@ -308,8 +308,8 @@ compute_MSigDB_enrichment <- function(membership_matrix, stop("membership_matrix values can't be <-1 or >1") } - m_df_simp <- msigdbr::msigdbr(species = "Homo sapiens") - gs_cat_levels <- sort(unique(m_df_simp$gs_cat)) + m_df_simp <- msigdbdf::msigdbdf(target_species = "HS") + gs_cat_levels <- sort(unique(m_df_simp$gs_collection)) if (all(!cats %in% gs_cat_levels)) { stop('No "cats" found in MSigDB. Must use at least one of: ', @@ -322,8 +322,8 @@ compute_MSigDB_enrichment <- function(membership_matrix, } sig_list <- lapply(cats, function(xx) { - tmp_data <- m_df_simp[m_df_simp$gs_cat == xx, ] - split(x = tmp_data$gene_symbol, f = tmp_data$gs_name) + tmp_data <- m_df_simp[m_df_simp$gs_collection == xx, ] + split(x = tmp_data$db_gene_symbol, f = tmp_data$gs_name) }) names(sig_list) <- cats @@ -924,7 +924,7 @@ display_top_genes <- function( #' results <- icwgcna(ex) #' #' unique_top_genes <- map_eigengenes_on_seurat( -#' SeuratObject::pbmc_small +#' SeuratObject::pbmc_small, #' results$community_membership #' ) #' } @@ -957,7 +957,7 @@ map_eigengenes_on_seurat <- function( message('Collecting signatures...') - if (cutoff_method %in% c('kme', 'both')) { + if (cutoff_method %in% c('value', 'both')) { genelist <- lapply( membership, diff --git a/man/map_eigengenes_on_seurat.Rd b/man/map_eigengenes_on_seurat.Rd index 5e75747..0b77907 100644 --- a/man/map_eigengenes_on_seurat.Rd +++ b/man/map_eigengenes_on_seurat.Rd @@ -67,7 +67,7 @@ ex <- as.matrix(data.table::fread(luad$destfiles), rownames = 1) results <- icwgcna(ex) unique_top_genes <- map_eigengenes_on_seurat( - SeuratObject::pbmc_small + SeuratObject::pbmc_small, results$community_membership ) } diff --git a/tests/testthat/_snaps/downstream.md b/tests/testthat/_snaps/downstream.md index 2a4bb08..e2f315b 100644 --- a/tests/testthat/_snaps/downstream.md +++ b/tests/testthat/_snaps/downstream.md @@ -842,330 +842,168 @@ AGTCTTACTTCGGA SeuratProject 157 29 0 GGAACACTTCAGAC SeuratProject 150 30 0 CTTGATTGATCTTC SeuratProject 233 76 1 - letter.idents groups RNA_snn_res.1 mA1_UCell mA2_UCell mA3_UCell - ATGCCAGAACGACT A g2 0 0.5151448 0.4053452 0.5634744 - CATGGCCTGTGCAT A g1 0 0.5452116 0.3942094 0.5922049 - GAACCTGATGAACC B g2 0 0.4939866 0.3986637 0.4939866 - TGACTGGATTCTCA A g2 0 0.4844098 0.3853007 0.4844098 - AGTCAGACTGCACA A g2 0 0.4476615 0.3919822 0.4476615 - TCTGATACACGTGT A g1 0 0.4031180 0.4031180 0.4512249 - TGGTATCTAAACAG A g1 0 0.5260579 0.4298441 0.5260579 - GCAGCTCTGTTTCT A g1 0 0.4708241 0.4097996 0.4708241 - GATATAACACGCAT A g1 0 0.4783964 0.4298441 0.5269488 - AATGTTGACAGTCA A g1 0 0.4783964 0.4187082 0.4783964 - AGGTCATGAGTGTC A g2 2 0.5376392 0.4893096 0.5859688 - AGAGATGATCTCGC A g1 2 0.5391982 0.5260579 0.5538976 - GGGTAACTCTAGTG A g2 2 0.5810690 0.4732739 0.5336303 - CATGAGACACGGGA A g2 2 0.5008909 0.5585746 0.5496659 - TACGCCACTCCGAA A g2 2 0.5149220 0.5162584 0.5149220 - CTAAACCTGTGCAT A g1 2 0.5750557 0.5630290 0.5287305 - GTAAGCACTCATTC A g2 2 0.5327394 0.5327394 0.5327394 - TTGGTACTGAATCC A g1 2 0.5233853 0.5155902 0.5703786 - CATCATACGGAGCA A g1 2 0.5193764 0.5706013 0.5679287 - TACATCACGCTAAC A g2 2 0.5229399 0.5817372 0.5229399 - TTACCATGAATCGC B g1 1 0.6287305 0.4082405 0.6336303 - ATAGGAGAAACAGA B g1 1 0.6305122 0.3452116 0.6434298 - GCGCACGACTTTAC B g2 1 0.5614699 0.4496659 0.6224944 - ACTCGCACGAAAGT B g2 1 0.5988864 0.4008909 0.6111359 - ATTACCTGCCTTAT B g1 1 0.4877506 0.3817372 0.5126949 - CCCAACTGCAATCG B g2 1 0.5113586 0.4164811 0.5717149 - AAATTCGAATCACG B g2 1 0.5069042 0.3719376 0.4817372 - CCATCCGATTCGCC B g2 1 0.5069042 0.4447661 0.5681514 - TCCACTCTGAGCTT B g2 1 0.5819599 0.3817372 0.5942094 - CATCAGGATGCACA B g1 1 0.6271715 0.3318486 0.6371938 - CTAAACCTCTGACA A g1 0 0.4897550 0.5614699 0.4302895 - GATAGAGAAGGGTG A g1 2 0.4993318 0.4955457 0.4418708 - CTAACGGAACCGAT A g1 0 0.4532294 0.4837416 0.4378619 - AGATATACCCGTAA A g2 0 0.4287305 0.5273942 0.3741648 - TACTCTGAATCGAC A g1 0 0.4619154 0.4630290 0.4574610 - GCGCATCTTGCTCC A g1 0 0.4612472 0.5104677 0.4053452 - GTTGACGATATCGG A g2 0 0.4672606 0.5461024 0.3608018 - ACAGGTACTGGTGT A g1 0 0.4864143 0.5554566 0.4685969 - GGCATATGCTTATC A g1 0 0.4485523 0.5469933 0.3919822 - CATTACACCAACTG A g2 0 0.4242762 0.5231626 0.3652561 - TAGGGACTGAACTC A g1 0 0.4828508 0.4815145 0.4220490 - GCTCCATGAGAAGT A g2 2 0.5630290 0.4213808 0.5630290 - TACAATGATGCTAG A g2 0 0.4692650 0.4659243 0.5160356 - CTTCATGACCGAAT A g2 0 0.4884187 0.4884187 0.4884187 - CTGCCAACAGGAGC A g1 2 0.4525612 0.4608018 0.4525612 - TTGCATTGAGCTAC A g2 2 0.5697105 0.4209354 0.5153675 - AAGCAAGAGCTTAG A g1 0 0.5109131 0.4621381 0.4501114 - CGGCACGAACTCAG A g2 0 0.4449889 0.4449889 0.4924276 - GGTGGAGATTACTC A g1 0 0.4505568 0.4478842 0.3942094 - GGCCGATGTACTCT A g2 0 0.5198218 0.5149220 0.5198218 - CGTAGCCTGTATGC B g1 1 0.5688196 0.3830735 0.5875278 - TGAGCTGAATGCTG B g2 1 0.5984410 0.4035635 0.6173719 - CCTATAACGAGACG B g2 2 0.5563474 0.4545657 0.5663697 - ATAAGTTGGTACGT B g2 1 0.5587973 0.4164811 0.5202673 - AAGCGACTTTGACG B g1 1 0.5051225 0.3385301 0.5149220 - ACCAGTGAATACCG A g1 1 0.5995546 0.3821826 0.6095768 - ATTGCACTTGCTTT B g1 1 0.5835189 0.3714922 0.5873051 - CTAGGTGATGGTTG B g1 1 0.6040089 0.3407572 0.6057906 - GCACTAGACCTTTA B g2 1 0.5648107 0.3924276 0.5732739 - CATGCGCTAGTCAC A g1 0 0.4935412 0.3692650 0.4935412 - TTGAGGACTACGCA A g1 2 0.5930958 0.3536748 0.6737194 - ATACCACTCTAAGC B g1 1 0.6082405 0.3563474 0.7425390 - CATATAGACTAAGC A g1 2 0.6342984 0.3585746 0.7534521 - TTTAGCTGTACTCT B g1 1 0.5670379 0.4318486 0.6412027 - GACATTCTCCACCT B g1 2 0.6240535 0.2962138 0.8013363 - ACGTGATGCCATGA B g2 1 0.6374165 0.3006682 0.7801782 - ATTGTAGATTCCCG B g2 1 0.5694878 0.3616927 0.6964365 - GATAGAGATCACGA B g1 1 0.6051225 0.3496659 0.7311804 - AATGCGTGGACGGA B g1 1 0.5184855 0.3893096 0.6360802 - GCGTAAACACGGTT A g1 2 0.5728285 0.3648107 0.6418708 - ATTCAGCTCATTGG A g2 0 0.5425390 0.4253898 0.5327394 - GGCATATGGGGAGT A g1 0 0.5532294 0.4454343 0.5425390 - ATCATCTGACACCA A g2 0 0.5452116 0.4795100 0.5316258 - GTCATACTTCGCCT A g2 0 0.5501114 0.5300668 0.4917595 - TTACGTACGTTCAG A g1 0 0.5394209 0.4685969 0.5251670 - GAGTTGTGGTAGCT A g1 0 0.5701559 0.4545657 0.5091314 - GACGCTCTCTCTCG A g2 0 0.5527840 0.4890869 0.4951002 - AGTCTTACTTCGGA A g1 0 0.5576837 0.4953229 0.5002227 - GGAACACTTCAGAC A g2 0 0.5547884 0.4933185 0.4971047 - CTTGATTGATCTTC B g1 1 0.6115813 0.3407572 0.6048998 - mA5_UCell mA6_UCell mA8_UCell mA10_UCell mA11_UCell mB1_UCell - ATGCCAGAACGACT 0.4053452 0.5020045 0.4053452 0.4536748 0.4053452 0.4053452 - CATGGCCTGTGCAT 0.4881960 0.5452116 0.4412027 0.3942094 0.3942094 0.4881960 - GAACCTGATGAACC 0.4463252 0.3986637 0.3986637 0.3986637 0.3986637 0.3986637 - TGACTGGATTCTCA 0.3853007 0.3853007 0.4302895 0.4752784 0.3853007 0.3853007 - AGTCAGACTGCACA 0.4380846 0.4380846 0.4380846 0.3919822 0.3919822 0.4380846 - TCTGATACACGTGT 0.4512249 0.4031180 0.4512249 0.4031180 0.4031180 0.4512249 - TGGTATCTAAACAG 0.4298441 0.4298441 0.4298441 0.4779510 0.4779510 0.4779510 - GCAGCTCTGTTTCT 0.4585746 0.4097996 0.4097996 0.4097996 0.4097996 0.4097996 - GATATAACACGCAT 0.4298441 0.4783964 0.4298441 0.4298441 0.4298441 0.4298441 - AATGTTGACAGTCA 0.4187082 0.4187082 0.4187082 0.4187082 0.4187082 0.4187082 - AGGTCATGAGTGTC 0.4893096 0.4893096 0.4409800 0.5939866 0.5995546 0.4409800 - AGAGATGATCTCGC 0.5260579 0.4193764 0.4193764 0.5412027 0.6265033 0.4193764 - GGGTAACTCTAGTG 0.4732739 0.5135857 0.4187082 0.5859688 0.6334076 0.4661470 - CATGAGACACGGGA 0.5585746 0.4521158 0.4521158 0.6630290 0.6699332 0.5053452 - TACGCCACTCCGAA 0.5162584 0.4097996 0.4567929 0.4650334 0.5714922 0.4097996 - CTAAACCTGTGCAT 0.5630290 0.4120267 0.4583519 0.6213808 0.6184855 0.4583519 - GTAAGCACTCATTC 0.5327394 0.4846325 0.4365256 0.6420935 0.6922049 0.4365256 - TTGGTACTGAATCC 0.5155902 0.4567929 0.4567929 0.5806236 0.6777283 0.4097996 - CATCATACGGAGCA 0.5706013 0.4142539 0.4142539 0.6178174 0.6850780 0.4628062 - TACATCACGCTAAC 0.5817372 0.4659243 0.4748330 0.6209354 0.7389755 0.4187082 - TTACCATGAATCGC 0.4732739 0.5251670 0.4688196 0.5140312 0.4280624 0.5256125 - ATAGGAGAAACAGA 0.4075724 0.4583519 0.3997773 0.5126949 0.4037862 0.4583519 - GCGCACGACTTTAC 0.5113586 0.5149220 0.4031180 0.4570156 0.5035635 0.5109131 - ACTCGCACGAAAGT 0.4623608 0.5048998 0.4505568 0.4452116 0.4452116 0.4895323 - ATTACCTGCCTTAT 0.4494432 0.4445434 0.3817372 0.4434298 0.4434298 0.4866370 - CCCAACTGCAATCG 0.4734967 0.4639198 0.4164811 0.4164811 0.4164811 0.4164811 - AAATTCGAATCACG 0.4363029 0.4169265 0.4169265 0.4169265 0.3719376 0.3719376 - CCATCCGATTCGCC 0.5069042 0.5069042 0.3986637 0.3986637 0.4447661 0.4527840 - TCCACTCTGAGCTT 0.4496659 0.4690423 0.3959911 0.4412027 0.4002227 0.4654788 - CATCAGGATGCACA 0.3988864 0.4984410 0.3884187 0.4253898 0.3839644 0.4360802 - CTAAACCTCTGACA 0.5002227 0.4342984 0.6253898 0.5057906 0.3786192 0.5559020 - GATAGAGAAGGGTG 0.5552339 0.3964365 0.6126949 0.5075724 0.3964365 0.6126949 - CTAACGGAACCGAT 0.4922049 0.4507795 0.6605791 0.5603563 0.3919822 0.6111359 - AGATATACCCGTAA 0.5723831 0.3741648 0.6926503 0.5576837 0.3741648 0.5895323 - TACTCTGAATCGAC 0.5556793 0.5100223 0.6173719 0.5710468 0.4031180 0.6020045 - GCGCATCTTGCTCC 0.5173719 0.5053452 0.6244989 0.5244989 0.4053452 0.5708241 - GTTGACGATATCGG 0.5868597 0.4184855 0.7712695 0.5478842 0.3608018 0.6579065 - ACAGGTACTGGTGT 0.5507795 0.4685969 0.7195991 0.5498886 0.3786192 0.5957684 - GGCATATGCTTATC 0.5563474 0.4391982 0.6659243 0.5149220 0.3919822 0.6035635 - CATTACACCAACTG 0.5400891 0.4084633 0.6995546 0.5436526 0.3652561 0.5926503 - TAGGGACTGAACTC 0.5374165 0.4220490 0.6175947 0.6073497 0.4220490 0.5536748 - GCTCCATGAGAAGT 0.4685969 0.4213808 0.4685969 0.4213808 0.3741648 0.5158129 - TACAATGATGCTAG 0.4659243 0.4120267 0.4120267 0.5126949 0.5126949 0.4587973 - CTTCATGACCGAAT 0.4884187 0.4387528 0.4966592 0.5463252 0.4884187 0.4387528 - CTGCCAACAGGAGC 0.5080178 0.4053452 0.4525612 0.4608018 0.4608018 0.4525612 - TTGCATTGAGCTAC 0.4209354 0.4209354 0.4209354 0.4209354 0.4209354 0.4209354 - AAGCAAGAGCTTAG 0.5189310 0.4501114 0.6380846 0.5812918 0.4031180 0.5801782 - CGGCACGAACTCAG 0.5024499 0.3875278 0.4924276 0.4924276 0.4449889 0.4449889 - GGTGGAGATTACTC 0.4478842 0.3942094 0.5650334 0.5650334 0.3942094 0.5086860 - GGCCGATGTACTCT 0.5619154 0.4648107 0.5037862 0.4679287 0.4679287 0.5037862 - CGTAGCCTGTATGC 0.4498886 0.4639198 0.3919822 0.3966592 0.3966592 0.4525612 - TGAGCTGAATGCTG 0.4661470 0.4884187 0.4035635 0.4527840 0.3251670 0.4643653 - CCTATAACGAGACG 0.5004454 0.5104677 0.4445434 0.4445434 0.3986637 0.4521158 - ATAAGTTGGTACGT 0.4164811 0.4639198 0.4639198 0.4164811 0.4164811 0.4164811 - AAGCGACTTTGACG 0.4011136 0.3959911 0.3930958 0.3873051 0.3385301 0.3385301 - ACCAGTGAATACCG 0.4378619 0.4527840 0.3986637 0.3821826 0.3429844 0.4008909 - ATTGCACTTGCTTT 0.4342984 0.4233853 0.4296214 0.4133630 0.3296214 0.3815145 - CTAGGTGATGGTTG 0.4013363 0.4378619 0.3995546 0.4334076 0.3407572 0.3966592 - GCACTAGACCTTTA 0.3924276 0.4498886 0.4062361 0.3924276 0.3518931 0.4008909 - CATGCGCTAGTCAC 0.3692650 0.3839644 0.4291759 0.3692650 0.3296214 0.3839644 - TTGAGGACTACGCA 0.3933185 0.4311804 0.4329621 0.5042316 0.3688196 0.4481069 - ATACCACTCTAAGC 0.3563474 0.4538976 0.3975501 0.5456570 0.4741648 0.4178174 - CATATAGACTAAGC 0.4026726 0.4694878 0.4026726 0.5641425 0.4565702 0.4026726 - TTTAGCTGTACTCT 0.4984410 0.4153675 0.3730512 0.5844098 0.5975501 0.3670379 - GACATTCTCCACCT 0.2962138 0.5057906 0.2962138 0.4855234 0.4037862 0.3913140 - ACGTGATGCCATGA 0.3712695 0.5728285 0.3385301 0.4877506 0.4135857 0.4080178 - ATTGTAGATTCCCG 0.4253898 0.4403118 0.3616927 0.5033408 0.4342984 0.4158129 - GATAGAGATCACGA 0.4162584 0.4521158 0.3496659 0.4928731 0.4955457 0.3930958 - AATGCGTGGACGGA 0.4538976 0.4089087 0.3474388 0.5073497 0.4928731 0.4006682 - GCGTAAACACGGTT 0.3648107 0.4044543 0.4044543 0.5957684 0.4665924 0.3873051 - ATTCAGCTCATTGG 0.4750557 0.5278396 0.4837416 0.4253898 0.4253898 0.4837416 - GGCATATGGGGAGT 0.4454343 0.5507795 0.5002227 0.4454343 0.4454343 0.5002227 - ATCATCTGACACCA 0.4276169 0.5378619 0.5365256 0.4276169 0.4276169 0.5365256 - GTCATACTTCGCCT 0.4848552 0.5427617 0.5866370 0.4365256 0.4365256 0.5866370 - TTACGTACGTTCAG 0.4231626 0.5298441 0.5269488 0.4231626 0.4231626 0.5269488 - GAGTTGTGGTAGCT 0.4053452 0.5173719 0.5062361 0.4053452 0.4053452 0.5062361 - GACGCTCTCTCTCG 0.4432071 0.5469933 0.5432071 0.4432071 0.4432071 0.5432071 - AGTCTTACTTCGGA 0.4454343 0.5469933 0.5472160 0.4454343 0.4454343 0.5472160 - GGAACACTTCAGAC 0.4432071 0.5432071 0.5472160 0.4432071 0.4432071 0.5472160 - CTTGATTGATCTTC 0.4057906 0.5053452 0.4476615 0.4409800 0.4409800 0.5095768 - mB2_UCell mB3_UCell mC1_UCell mC2_UCell mC3_UCell mC5_UCell - ATGCCAGAACGACT 0.4536748 0.5020045 0.4053452 0.4053452 0.4053452 0.5503341 - CATGGCCTGTGCAT 0.4982183 0.5452116 0.4412027 0.4412027 0.4412027 0.4881960 - GAACCTGATGAACC 0.3986637 0.3986637 0.3986637 0.3986637 0.3986637 0.4463252 - TGACTGGATTCTCA 0.3853007 0.4302895 0.3853007 0.4302895 0.3853007 0.3853007 - AGTCAGACTGCACA 0.4380846 0.4841871 0.4380846 0.4380846 0.4380846 0.3919822 - TCTGATACACGTGT 0.4031180 0.4512249 0.4512249 0.4512249 0.4512249 0.4512249 - TGGTATCTAAACAG 0.4298441 0.4298441 0.4298441 0.4298441 0.4298441 0.4779510 - GCAGCTCTGTTTCT 0.4097996 0.4585746 0.4097996 0.4097996 0.4097996 0.4097996 - GATATAACACGCAT 0.4298441 0.4298441 0.4298441 0.4298441 0.4298441 0.5269488 - AATGTTGACAGTCA 0.4187082 0.4663697 0.4187082 0.4187082 0.4187082 0.4187082 - AGGTCATGAGTGTC 0.4409800 0.5432071 0.4409800 0.4409800 0.4973274 0.6342984 - AGAGATGATCTCGC 0.3741648 0.5812918 0.5260579 0.3741648 0.4193764 0.6111359 - GGGTAACTCTAGTG 0.5135857 0.5314031 0.5207127 0.4661470 0.5207127 0.5300668 - CATGAGACACGGGA 0.4521158 0.6142539 0.5585746 0.4521158 0.5077951 0.5541203 - TACGCCACTCCGAA 0.4097996 0.5714922 0.5162584 0.4097996 0.4567929 0.5701559 - CTAAACCTGTGCAT 0.4583519 0.6184855 0.5167038 0.4583519 0.4120267 0.5287305 - GTAAGCACTCATTC 0.4365256 0.5884187 0.4846325 0.4365256 0.4922049 0.5864143 - TTGGTACTGAATCC 0.4097996 0.5734967 0.5155902 0.4097996 0.5140312 0.6133630 - CATCATACGGAGCA 0.4142539 0.5786192 0.5220490 0.4142539 0.4721604 0.5679287 - TACATCACGCTAAC 0.4187082 0.6378619 0.5345212 0.4187082 0.5287305 0.5296214 - TTACCATGAATCGC 0.4804009 0.3652561 0.4082405 0.4688196 0.4082405 0.4930958 - ATAGGAGAAACAGA 0.4543430 0.3452116 0.3452116 0.3997773 0.3452116 0.6327394 - GCGCACGACTTTAC 0.4570156 0.4496659 0.4496659 0.4031180 0.4031180 0.5685969 - ACTCGCACGAAAGT 0.4948775 0.4008909 0.4008909 0.4505568 0.4008909 0.5668151 - ATTACCTGCCTTAT 0.3817372 0.3817372 0.3817372 0.3817372 0.3385301 0.4694878 - CCCAACTGCAATCG 0.4164811 0.4164811 0.4164811 0.4164811 0.4164811 0.5242762 - AAATTCGAATCACG 0.4619154 0.3719376 0.4169265 0.4619154 0.4169265 0.5267261 - CCATCCGATTCGCC 0.4527840 0.4447661 0.4447661 0.3986637 0.3986637 0.5140312 - TCCACTCTGAGCTT 0.4612472 0.3407572 0.3407572 0.3959911 0.3817372 0.5699332 - CATCAGGATGCACA 0.4819599 0.3732739 0.3732739 0.3884187 0.4253898 0.5022272 - CTAAACCTCTGACA 0.5550111 0.4369710 0.6209354 0.6848552 0.5576837 0.3786192 - GATAGAGAAGGGTG 0.4538976 0.5015590 0.6126949 0.6701559 0.5590200 0.4418708 - CTAACGGAACCGAT 0.5579065 0.4463252 0.5993318 0.7218263 0.5534521 0.4378619 - AGATATACCCGTAA 0.4737194 0.4641425 0.6269488 0.7472160 0.5636971 0.3741648 - TACTCTGAATCGAC 0.5082405 0.4494432 0.5681514 0.6761693 0.5082405 0.5180401 - GCGCATCTTGCTCC 0.5612472 0.4587973 0.6198218 0.6804009 0.6077951 0.4053452 - GTTGACGATATCGG 0.5861915 0.4786192 0.6659243 0.8334076 0.6020045 0.3608018 - ACAGGTACTGGTGT 0.5011136 0.4886414 0.6732739 0.7824053 0.6111359 0.5135857 - GGCATATGCTTATC 0.5429844 0.4957684 0.6601336 0.7224944 0.5995546 0.3919822 - CATTACACCAACTG 0.4674833 0.4779510 0.6423163 0.7585746 0.5801782 0.4084633 - TAGGGACTGAACTC 0.4371938 0.4322940 0.5525612 0.6783964 0.4930958 0.4220490 - GCTCCATGAGAAGT 0.4685969 0.4685969 0.5158129 0.5158129 0.5158129 0.4685969 - TACAATGATGCTAG 0.4120267 0.4120267 0.4120267 0.4120267 0.4120267 0.4587973 - CTTCATGACCGAAT 0.4387528 0.4387528 0.4387528 0.4966592 0.4387528 0.4387528 - CTGCCAACAGGAGC 0.4053452 0.4525612 0.4525612 0.4525612 0.4525612 0.4053452 - TTGCATTGAGCTAC 0.4752784 0.4209354 0.4752784 0.4752784 0.4752784 0.4681514 - AAGCAAGAGCTTAG 0.4639198 0.4599109 0.5797327 0.6988864 0.5207127 0.4501114 - CGGCACGAACTCAG 0.3875278 0.4449889 0.4449889 0.4924276 0.4449889 0.4349666 - GGTGGAGATTACTC 0.4505568 0.3942094 0.5042316 0.6213808 0.4505568 0.3942094 - GGCCGATGTACTCT 0.4097996 0.5037862 0.5037862 0.5037862 0.5037862 0.4648107 - CGTAGCCTGTATGC 0.4478842 0.3429844 0.3429844 0.3919822 0.3830735 0.5316258 - TGAGCTGAATGCTG 0.4643653 0.3643653 0.3643653 0.4035635 0.3643653 0.5465479 - CCTATAACGAGACG 0.4979955 0.3986637 0.3986637 0.4445434 0.4545657 0.5587973 - ATAAGTTGGTACGT 0.5113586 0.4164811 0.4639198 0.5113586 0.4639198 0.5202673 - AAGCGACTTTGACG 0.3930958 0.3385301 0.3385301 0.3930958 0.3385301 0.5636971 - ACCAGTGAATACCG 0.4565702 0.3429844 0.3429844 0.3986637 0.3821826 0.5124722 - ATTGCACTTGCTTT 0.4396437 0.3296214 0.3296214 0.4296214 0.3714922 0.5354120 - CTAGGTGATGGTTG 0.4554566 0.3407572 0.3407572 0.3995546 0.3407572 0.5910913 - GCACTAGACCTTTA 0.4552339 0.3518931 0.3518931 0.4062361 0.3924276 0.5648107 - CATGCGCTAGTCAC 0.4438753 0.3296214 0.3296214 0.4291759 0.3692650 0.4391982 - TTGAGGACTACGCA 0.3536748 0.3933185 0.3933185 0.4329621 0.3933185 0.6962138 - ATACCACTCTAAGC 0.3975501 0.3563474 0.3563474 0.3975501 0.3563474 0.7610245 - CATATAGACTAAGC 0.3585746 0.3585746 0.3585746 0.4026726 0.3585746 0.7501114 - TTTAGCTGTACTCT 0.3730512 0.4318486 0.3832962 0.3730512 0.3770601 0.6543430 - GACATTCTCCACCT 0.3345212 0.2962138 0.2962138 0.2962138 0.2962138 0.7839644 - ACGTGATGCCATGA 0.3877506 0.3006682 0.3006682 0.3385301 0.3498886 0.7730512 - ATTGTAGATTCCCG 0.3229399 0.3616927 0.3616927 0.3616927 0.3616927 0.7494432 - GATAGAGATCACGA 0.3496659 0.3930958 0.3496659 0.3496659 0.3496659 0.7616927 - AATGCGTGGACGGA 0.3474388 0.3893096 0.3893096 0.3474388 0.3474388 0.6300668 - GCGTAAACACGGTT 0.4440980 0.3251670 0.3648107 0.4440980 0.3648107 0.6636971 - ATTCAGCTCATTGG 0.5957684 0.4797327 0.5380846 0.4837416 0.5244989 0.5247216 - GGCATATGGGGAGT 0.5973274 0.4919822 0.5467706 0.5002227 0.5467706 0.5385301 - ATCATCTGACACCA 0.6489978 0.4817372 0.5387528 0.5365256 0.5855234 0.5273942 - GTCATACTTCGCCT 0.6418708 0.5331849 0.5897550 0.5866370 0.6293987 0.4817372 - TTACGTACGTTCAG 0.6378619 0.4775056 0.5358575 0.5269488 0.5730512 0.5213808 - GAGTTGTGGTAGCT 0.6100223 0.4498886 0.5015590 0.5062361 0.5518931 0.4587973 - GACGCTCTCTCTCG 0.6492205 0.4973274 0.5514477 0.5432071 0.5951002 0.4432071 - AGTCTTACTTCGGA 0.6487751 0.4922049 0.5440980 0.5472160 0.5888641 0.5013363 - GGAACACTTCAGAC 0.6011136 0.4432071 0.4971047 0.5472160 0.5394209 0.4917595 - CTTGATTGATCTTC 0.5587973 0.3407572 0.3942094 0.4476615 0.3942094 0.5363029 - mC6_UCell mC7_UCell mC9_UCell - ATGCCAGAACGACT 0.4053452 0.4668151 0.4668151 - CATGGCCTGTGCAT 0.4881960 0.4982183 0.4982183 - GAACCTGATGAACC 0.3986637 0.5416481 0.5416481 - TGACTGGATTCTCA 0.4302895 0.4844098 0.4844098 - AGTCAGACTGCACA 0.4380846 0.4476615 0.4476615 - TCTGATACACGTGT 0.4512249 0.4031180 0.4031180 - TGGTATCTAAACAG 0.4298441 0.4779510 0.4779510 - GCAGCTCTGTTTCT 0.4097996 0.5195991 0.5195991 - GATATAACACGCAT 0.4298441 0.4298441 0.4298441 - AATGTTGACAGTCA 0.4187082 0.4783964 0.4783964 - AGGTCATGAGTGTC 0.4409800 0.4409800 0.4409800 - AGAGATGATCTCGC 0.3741648 0.4193764 0.4193764 - GGGTAACTCTAGTG 0.4187082 0.4661470 0.4661470 - CATGAGACACGGGA 0.4521158 0.4521158 0.4521158 - TACGCCACTCCGAA 0.4097996 0.4567929 0.4567929 - CTAAACCTGTGCAT 0.4120267 0.4120267 0.4120267 - GTAAGCACTCATTC 0.4365256 0.4365256 0.4365256 - TTGGTACTGAATCC 0.4097996 0.4097996 0.4097996 - CATCATACGGAGCA 0.4142539 0.4628062 0.4628062 - TACATCACGCTAAC 0.4187082 0.4187082 0.4187082 - TTACCATGAATCGC 0.4628062 0.5808463 0.5808463 - ATAGGAGAAACAGA 0.3997773 0.4643653 0.4643653 - GCGCACGACTTTAC 0.4570156 0.5258352 0.5258352 - ACTCGCACGAAAGT 0.4452116 0.5184855 0.5184855 - ATTACCTGCCTTAT 0.4249443 0.5594655 0.5162584 - CCCAACTGCAATCG 0.4164811 0.5804009 0.5804009 - AAATTCGAATCACG 0.3719376 0.4997773 0.4997773 - CCATCCGATTCGCC 0.4527840 0.5224944 0.5224944 - TCCACTCTGAGCTT 0.4469933 0.5153675 0.5153675 - CATCAGGATGCACA 0.4253898 0.5046771 0.5567929 - CTAAACCTCTGACA 0.6253898 0.7153675 0.5937639 - GATAGAGAAGGGTG 0.5552339 0.4955457 0.3964365 - CTAACGGAACCGAT 0.6004454 0.5590200 0.5131403 - AGATATACCCGTAA 0.6305122 0.5855234 0.4772829 - TACTCTGAATCGAC 0.5710468 0.6173719 0.5574610 - GCGCATCTTGCTCC 0.6244989 0.6244989 0.6124722 - GTTGACGATATCGG 0.6692650 0.6523385 0.5282851 - ACAGGTACTGGTGT 0.6746102 0.5599109 0.4427617 - GGCATATGCTTATC 0.6659243 0.6093541 0.5015590 - CATTACACCAACTG 0.6469933 0.5436526 0.4289532 - TAGGGACTGAACTC 0.5556793 0.4997773 0.4403118 - GCTCCATGAGAAGT 0.5158129 0.4685969 0.4213808 - TACAATGATGCTAG 0.4120267 0.4692650 0.4692650 - CTTCATGACCGAAT 0.4966592 0.5463252 0.5463252 - CTGCCAACAGGAGC 0.4525612 0.4525612 0.4525612 - TTGCATTGAGCTAC 0.4209354 0.4681514 0.4681514 - AAGCAAGAGCTTAG 0.5768374 0.5200445 0.4610245 - CGGCACGAACTCAG 0.4924276 0.4924276 0.4924276 - GGTGGAGATTACTC 0.5042316 0.5042316 0.4505568 - GGCCGATGTACTCT 0.5037862 0.5118040 0.4648107 - CGTAGCCTGTATGC 0.4389755 0.4988864 0.4988864 - TGAGCTGAATGCTG 0.4643653 0.5545657 0.5153675 - CCTATAACGAGACG 0.5080178 0.5004454 0.5004454 - ATAAGTTGGTACGT 0.4164811 0.4741648 0.4741648 - AAGCGACTTTGACG 0.3385301 0.4556793 0.4556793 - ACCAGTGAATACCG 0.4400891 0.4378619 0.4378619 - ATTGCACTTGCTTT 0.4652561 0.5180401 0.5180401 - CTAGGTGATGGTTG 0.3966592 0.4425390 0.4425390 - GCACTAGACCTTTA 0.4414254 0.4414254 0.4414254 - CATGCGCTAGTCAC 0.4632517 0.4089087 0.4089087 - TTGAGGACTACGCA 0.3933185 0.3933185 0.3536748 - ATACCACTCTAAGC 0.3563474 0.4465479 0.4465479 - CATATAGACTAAGC 0.4026726 0.4908686 0.4908686 - TTTAGCTGTACTCT 0.3184855 0.4336303 0.4336303 - GACATTCTCCACCT 0.3345212 0.3728285 0.3728285 - ACGTGATGCCATGA 0.3498886 0.4354120 0.4846325 - ATTGTAGATTCCCG 0.3616927 0.4641425 0.4253898 - GATAGAGATCACGA 0.3496659 0.5258352 0.5258352 - AATGCGTGGACGGA 0.3474388 0.4683742 0.4683742 - GCGTAAACACGGTT 0.3648107 0.3648107 0.4044543 - ATTCAGCTCATTGG 0.5380846 0.5345212 0.6369710 - GGCATATGGGGAGT 0.5467706 0.5492205 0.6545657 - ATCATCTGACACCA 0.5906459 0.5387528 0.6489978 - GTCATACTTCGCCT 0.6349666 0.5884187 0.6463252 - TTACGTACGTTCAG 0.5812918 0.5282851 0.6349666 - GAGTTGTGGTAGCT 0.5507795 0.6046771 0.7167038 - GACGCTCTCTCTCG 0.5973274 0.5467706 0.6505568 - AGTCTTACTTCGGA 0.5939866 0.5527840 0.6543430 - GGAACACTTCAGAC 0.5472160 0.5510022 0.6510022 - CTTGATTGATCTTC 0.4518931 0.5229399 0.6298441 + letter.idents groups RNA_snn_res.1 mA1_UCell mA11_UCell + ATGCCAGAACGACT A g2 0 0.3991228 0.4026549 + CATGGCCTGTGCAT A g1 0 0.5423977 0.3915929 + GAACCTGATGAACC B g2 0 0.3925439 0.3960177 + TGACTGGATTCTCA A g2 0 0.3793860 0.3827434 + AGTCAGACTGCACA A g2 0 0.3859649 0.3893805 + TCTGATACACGTGT A g1 0 0.3969298 0.4004425 + TGGTATCTAAACAG A g1 0 0.4232456 0.4269912 + GCAGCTCTGTTTCT A g1 0 0.4035088 0.4070796 + GATATAACACGCAT A g1 0 0.4232456 0.4269912 + AATGTTGACAGTCA A g1 0 0.4122807 0.4159292 + AGGTCATGAGTGTC A g2 2 0.4342105 0.6630847 + AGAGATGATCTCGC A g1 2 0.3684211 0.6656131 + GGGTAACTCTAGTG A g2 2 0.5679825 0.6532870 + CATGAGACACGGGA A g2 2 0.4451754 0.7582174 + TACGCCACTCCGAA A g2 2 0.4035088 0.6365360 + CTAAACCTGTGCAT A g1 2 0.4057018 0.7022756 + GTAAGCACTCATTC A g2 2 0.4298246 0.7281922 + TTGGTACTGAATCC A g1 2 0.4035088 0.7206068 + CATCATACGGAGCA A g1 2 0.4078947 0.7958281 + TACATCACGCTAAC A g2 2 0.4122807 0.8034134 + TTACCATGAATCGC B g1 1 0.5387427 0.3628319 + ATAGGAGAAACAGA B g1 1 0.5190058 0.3429204 + GCGCACGACTTTAC B g2 1 0.5738304 0.4664981 + ACTCGCACGAAAGT B g2 1 0.5402047 0.3982301 + ATTACCTGCCTTAT B g1 1 0.4751462 0.3975980 + CCCAACTGCAATCG B g2 1 0.4100877 0.4137168 + AAATTCGAATCACG B g2 1 0.5138889 0.3694690 + CCATCCGATTCGCC B g2 1 0.5701754 0.4614412 + TCCACTCTGAGCTT B g2 1 0.5497076 0.3384956 + CATCAGGATGCACA B g1 1 0.4978070 0.3296460 + CTAAACCTCTGACA A g1 0 0.5679825 0.3761062 + GATAGAGAAGGGTG A g1 2 0.5789474 0.3938053 + CTAACGGAACCGAT A g1 0 0.5869883 0.3893805 + AGATATACCCGTAA A g2 0 0.5475146 0.3716814 + TACTCTGAATCGAC A g1 0 0.5899123 0.4004425 + GCGCATCTTGCTCC A g1 0 0.5826023 0.4026549 + GTTGACGATATCGG A g2 0 0.5592105 0.3584071 + ACAGGTACTGGTGT A g1 0 0.5789474 0.3761062 + GGCATATGCTTATC A g1 0 0.5716374 0.3893805 + CATTACACCAACTG A g2 0 0.5533626 0.3628319 + TAGGGACTGAACTC A g1 0 0.5701754 0.4386852 + GCTCCATGAGAAGT A g2 2 0.6783626 0.3716814 + TACAATGATGCTAG A g2 0 0.4057018 0.4857775 + CTTCATGACCGAAT A g2 0 0.4320175 0.5063211 + CTGCCAACAGGAGC A g1 2 0.3991228 0.4813527 + TTGCATTGAGCTAC A g2 2 0.5928363 0.4181416 + AAGCAAGAGCTTAG A g1 0 0.5964912 0.4004425 + CGGCACGAACTCAG A g2 0 0.3815789 0.4664981 + GGTGGAGATTACTC A g1 0 0.5730994 0.3915929 + GGCCGATGTACTCT A g2 0 0.4035088 0.4895702 + CGTAGCCTGTATGC B g1 1 0.5211988 0.3407080 + TGAGCTGAATGCTG B g2 1 0.5197368 0.3230088 + CCTATAACGAGACG B g2 2 0.5679825 0.3960177 + ATAAGTTGGTACGT B g2 1 0.5657895 0.4137168 + AAGCGACTTTGACG B g1 1 0.3333333 0.3362832 + ACCAGTGAATACCG A g1 1 0.5277778 0.3407080 + ATTGCACTTGCTTT B g1 1 0.4948830 0.3274336 + CTAGGTGATGGTTG B g1 1 0.5190058 0.3384956 + GCACTAGACCTTTA B g2 1 0.5073099 0.3495575 + CATGCGCTAGTCAC A g1 0 0.5029240 0.3274336 + TTGAGGACTACGCA A g1 2 0.3092105 0.3119469 + ATACCACTCTAAGC B g1 1 0.3508772 0.3539823 + CATATAGACTAAGC A g1 2 0.3530702 0.3561947 + TTTAGCTGTACTCT B g1 1 0.3135965 0.5603666 + GACATTCTCCACCT B g1 2 0.4173977 0.2942478 + ACGTGATGCCATGA B g2 1 0.4576023 0.2986726 + ATTGTAGATTCCCG B g2 1 0.3179825 0.3207965 + GATAGAGATCACGA B g1 1 0.3442982 0.4089760 + AATGCGTGGACGGA B g1 1 0.3421053 0.4045512 + GCGTAAACACGGTT A g1 2 0.5804094 0.3792668 + ATTCAGCTCATTGG A g2 0 0.6081871 0.4225664 + GGCATATGGGGAGT A g1 0 0.6045322 0.4424779 + ATCATCTGACACCA A g2 0 0.6125731 0.4247788 + GTCATACTTCGCCT A g2 0 0.6111111 0.4336283 + TTACGTACGTTCAG A g1 0 0.6023392 0.4203540 + GAGTTGTGGTAGCT A g1 0 0.5935673 0.4026549 + GACGCTCTCTCTCG A g2 0 0.6067251 0.4402655 + AGTCTTACTTCGGA A g1 0 0.6184211 0.4424779 + GGAACACTTCAGAC A g2 0 0.6133041 0.4402655 + CTTGATTGATCTTC B g1 1 0.7002924 0.3384956 + mC5_UCell + ATGCCAGAACGACT 0.3991228 + CATGGCCTGTGCAT 0.3881579 + GAACCTGATGAACC 0.3925439 + TGACTGGATTCTCA 0.3793860 + AGTCAGACTGCACA 0.3859649 + TCTGATACACGTGT 0.3969298 + TGGTATCTAAACAG 0.4232456 + GCAGCTCTGTTTCT 0.4035088 + GATATAACACGCAT 0.4232456 + AATGTTGACAGTCA 0.4122807 + AGGTCATGAGTGTC 0.4342105 + AGAGATGATCTCGC 0.3684211 + GGGTAACTCTAGTG 0.4122807 + CATGAGACACGGGA 0.4451754 + TACGCCACTCCGAA 0.4035088 + CTAAACCTGTGCAT 0.4057018 + GTAAGCACTCATTC 0.4298246 + TTGGTACTGAATCC 0.4035088 + CATCATACGGAGCA 0.4078947 + TACATCACGCTAAC 0.4122807 + TTACCATGAATCGC 0.3596491 + ATAGGAGAAACAGA 0.3399123 + GCGCACGACTTTAC 0.3969298 + ACTCGCACGAAAGT 0.3947368 + ATTACCTGCCTTAT 0.3333333 + CCCAACTGCAATCG 0.4100877 + AAATTCGAATCACG 0.3662281 + CCATCCGATTCGCC 0.3925439 + TCCACTCTGAGCTT 0.3355263 + CATCAGGATGCACA 0.3267544 + CTAAACCTCTGACA 0.3728070 + GATAGAGAAGGGTG 0.3903509 + CTAACGGAACCGAT 0.3859649 + AGATATACCCGTAA 0.3684211 + TACTCTGAATCGAC 0.5957602 + GCGCATCTTGCTCC 0.3991228 + GTTGACGATATCGG 0.3552632 + ACAGGTACTGGTGT 0.5204678 + GGCATATGCTTATC 0.3859649 + CATTACACCAACTG 0.5014620 + TAGGGACTGAACTC 0.5204678 + GCTCCATGAGAAGT 0.3684211 + TACAATGATGCTAG 0.4057018 + CTTCATGACCGAAT 0.4320175 + CTGCCAACAGGAGC 0.3991228 + TTGCATTGAGCTAC 0.4144737 + AAGCAAGAGCTTAG 0.3969298 + CGGCACGAACTCAG 0.3815789 + GGTGGAGATTACTC 0.3881579 + GGCCGATGTACTCT 0.4035088 + CGTAGCCTGTATGC 0.3377193 + TGAGCTGAATGCTG 0.3201754 + CCTATAACGAGACG 0.3925439 + ATAAGTTGGTACGT 0.4100877 + AAGCGACTTTGACG 0.3333333 + ACCAGTGAATACCG 0.3377193 + ATTGCACTTGCTTT 0.3245614 + CTAGGTGATGGTTG 0.3355263 + GCACTAGACCTTTA 0.3464912 + CATGCGCTAGTCAC 0.3245614 + TTGAGGACTACGCA 0.6937135 + ATACCACTCTAAGC 0.6710526 + CATATAGACTAAGC 0.5299708 + TTTAGCTGTACTCT 0.5058480 + GACATTCTCCACCT 0.6871345 + ACGTGATGCCATGA 0.6754386 + ATTGTAGATTCCCG 0.5153509 + GATAGAGATCACGA 0.5380117 + AATGCGTGGACGGA 0.5438596 + GCGTAAACACGGTT 0.4502924 + ATTCAGCTCATTGG 0.4188596 + GGCATATGGGGAGT 0.4385965 + ATCATCTGACACCA 0.4210526 + GTCATACTTCGCCT 0.4298246 + TTACGTACGTTCAG 0.4166667 + GAGTTGTGGTAGCT 0.3991228 + GACGCTCTCTCTCG 0.4364035 + AGTCTTACTTCGGA 0.4385965 + GGAACACTTCAGAC 0.4364035 + CTTGATTGATCTTC 0.3355263 # map_eigengenes_on_seurat prefix and both method diff --git a/tests/testthat/fixtures/testing_MSigDB_enrichment.rds b/tests/testthat/fixtures/testing_MSigDB_enrichment.rds index d98b9b8..f509311 100644 Binary files a/tests/testthat/fixtures/testing_MSigDB_enrichment.rds and b/tests/testthat/fixtures/testing_MSigDB_enrichment.rds differ diff --git a/tests/testthat/test-downstream.R b/tests/testthat/test-downstream.R index 53055af..1946d5a 100644 --- a/tests/testthat/test-downstream.R +++ b/tests/testthat/test-downstream.R @@ -136,7 +136,7 @@ test_that('requireNamespace stubbing (MSigDB)', { expect_error( compute_MSigDB_enrichment(testing_results$community_membership), - "Must have the following R packages installed for this function: msigdbr, foreach, tidyr") + "Must have the following R packages installed for this function: msigdbdf, foreach, tidyr") })