hectorrdb / bioc2021trajectories

Repository for the Bioc2021 workshop.

DailyHRB

This is a package to load useful functions that I use on a daily basis. It also contains a template for an Rmd and RStudio Project template. You can install it from Github with the following:

if (!"devtools" %in% installed.packages()) {
  install.pacakges("devtools")
}
devtools::install_github("HectorRDB/DailyHRB")

or from source with

git clone [email protected]:HectorRDB/DailyHRB.git
R CMD INSTALL DailyHRB

bioc2021trajectories's Issues

Cannot reproduce bioc2021trajectories workshop: Error in .local(counts, ...) :

Hi,

I cannot reproduce the Bioc2021trajectories tutorial.

When I run:
icMat <- evaluateK(counts = as.matrix(assays(tgfb)$counts), pseudotime = colData(tgfb)$slingshot$pseudotime, cellWeights = colData(tgfb)$slingshot$cellWeights.V1, conditions = factor(colData(tgfb)$pheno$treatment_id), nGenes = 300, k = 3:7)

I get:
Error in .local(counts, ...) : Either provide the slingshot object using the sds argument, or provide pseudotime and cell-level weights manually using pseudotime and cellWeights arguments.

My session:

`sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 20.1

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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=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 grid stats graphics grDevices utils
[8] datasets methods base

other attached packages:
[1] tradeSeq_1.4.0 slingshot_1.99.12
[3] TrajectoryUtils_0.99.2 princurve_2.1.6
[5] condimentsPaper_1.0 condiments_1.1.04
[7] clustree_0.4.3 ggraph_2.0.5
[9] harmony_1.0 ggthemes_4.2.4
[11] lemon_0.4.5 ggrepel_0.9.1
[13] scran_1.18.7 scater_1.18.6
[15] SingleCellExperiment_1.12.0 DESeq2_1.30.1
[17] SummarizedExperiment_1.20.0 Biobase_2.50.0
[19] MatrixGenerics_1.2.1 matrixStats_0.58.0
[21] GenomicRanges_1.42.0 GenomeInfoDb_1.26.7
[23] IRanges_2.24.1 S4Vectors_0.28.1
[25] BiocGenerics_0.36.1 fgsea_1.16.0
[27] enrichR_3.0 survminer_0.4.9
[29] ggpubr_0.4.0 survival_3.2-11
[31] GSVA_1.38.2 plotly_4.9.3
[33] future.apply_1.7.0 future_1.21.0
[35] presto_1.0.0 Rcpp_1.0.6
[37] ggvenn_0.1.9 ggVennDiagram_1.1.5
[39] msigdbr_7.2.1 readxl_1.3.1
[41] ComplexHeatmap_2.6.2 ggsci_2.9
[43] RColorBrewer_1.1-2 data.table_1.14.0
[45] forcats_0.5.1 stringr_1.4.0
[47] dplyr_1.0.5 purrr_0.3.4
[49] readr_1.4.0 tidyr_1.1.3
[51] tibble_3.1.4 ggplot2_3.3.3
[53] tidyverse_1.3.1 SeuratObject_4.0.1
[55] Seurat_4.0.1

loaded via a namespace (and not attached):
[1] Ecume_0.9.1 spatstat.linnet_2.1-1
[3] graphlayouts_0.7.1 pbapply_1.4-3
[5] lattice_0.20-44 haven_2.4.0
[7] vctrs_0.3.8 fastICA_1.2-2
[9] usethis_2.0.1 mgcv_1.8-36
[11] flowCore_2.2.0 blob_1.2.1
[13] prodlim_2019.11.13 dynutils_1.0.6
[15] spatstat.data_2.1-0 later_1.1.0.1
[17] DBI_1.1.1 R.utils_2.10.1
[19] uwot_0.1.10 dqrng_0.2.1
[21] jpeg_0.1-8.1 zlibbioc_1.36.0
[23] htmlwidgets_1.5.3 GlobalOptions_0.1.2
[25] leiden_0.3.7 lmds_0.1.0
[27] irlba_2.3.3 markdown_1.1
[29] tidygraph_1.2.0 KernSmooth_2.23-20
[31] promises_1.2.0.1 DDRTree_0.1.5
[33] DelayedArray_0.16.3 limma_3.46.0
[35] pkgload_1.2.1 magick_2.7.2
[37] graph_1.68.0 RcppParallel_5.1.2
[39] Hmisc_4.5-0 RSpectra_0.16-0
[41] fs_1.5.0 fastmatch_1.1-0
[43] digest_0.6.27 png_0.1-7
[45] bluster_1.0.0 qlcMatrix_0.9.7
[47] sctransform_0.3.2 cowplot_1.1.1
[49] glmnet_4.1-1 docopt_0.7.1
[51] pkgconfig_2.0.3 DelayedMatrixStats_1.12.3
[53] gower_0.2.2 ggbeeswarm_0.6.0
[55] iterators_1.0.13 DropletUtils_1.10.3
[57] reticulate_1.18 DAseq_1.0.0
[59] circlize_0.4.12 beeswarm_0.3.1
[61] GetoptLong_1.0.5 xfun_0.22
[63] zoo_1.8-9 tidyselect_1.1.0
[65] reshape2_1.4.4 kernlab_0.9-29
[67] ica_1.0-2 bioc2021trajectories_0.0.21
[69] viridisLite_0.4.0 miloR_0.99.8
[71] pkgbuild_1.2.0 rlang_0.4.10
[73] spatstat_2.1-0 RVenn_1.1.0
[75] glue_1.4.2 modelr_0.1.8
[77] lava_1.6.9 RProtoBufLib_2.2.0
[79] ggsignif_0.6.1 recipes_0.1.16
[81] labeling_0.4.2 httpuv_1.5.5
[83] class_7.3-19 BiocNeighbors_1.8.2
[85] annotate_1.68.0 jsonlite_1.7.2
[87] XVector_0.30.0 bit_4.0.4
[89] mime_0.10 GillespieSSA2_0.2.7
[91] gridExtra_2.3 stringi_1.5.3
[93] processx_3.5.1 spatstat.sparse_2.0-0
[95] scattermore_0.7 bitops_1.0-6
[97] cli_3.0.1 rhdf5filters_1.2.0
[99] RSQLite_2.2.6 pheatmap_1.0.12
[101] rstudioapi_0.13 nlme_3.1-152
[103] locfit_1.5-9.4 listenv_0.8.0
[105] miniUI_0.1.1.1 survMisc_0.5.5
[107] R.oo_1.24.0 dbplyr_2.1.1
[109] sessioninfo_1.1.1 lifecycle_1.0.0
[111] timeDate_3043.102 transport_0.12-2
[113] munsell_0.5.0 cellranger_1.1.0
[115] R.methodsS3_1.8.1 proxyC_0.1.5
[117] codetools_0.2-18 vipor_0.4.5
[119] lmtest_0.9-38 htmlTable_2.1.0
[121] xtable_1.8-4 ROCR_1.0-11
[123] BiocManager_1.30.12 abind_1.4-5
[125] FNN_1.1.3 farver_2.1.0
[127] parallelly_1.24.0 km.ci_0.5-2
[129] RANN_2.6.1 sparsesvd_0.2
[131] GEOquery_2.58.0 RcppAnnoy_0.0.18
[133] goftest_1.2-2 patchwork_1.1.1
[135] cluster_2.1.2 Matrix_1.3-4
[137] ellipsis_0.3.2 prettyunits_1.1.1
[139] lubridate_1.7.10 ggridges_0.5.3
[141] reprex_2.0.0 igraph_1.2.6
[143] slam_0.1-48 remotes_2.3.0
[145] testthat_3.0.2 spatstat.utils_2.1-0
[147] htmltools_0.5.1.1 utf8_1.2.1
[149] XML_3.99-0.6 ModelMetrics_1.2.2.2
[151] e1071_1.7-6 foreign_0.8-81
[153] withr_2.4.1 scuttle_1.0.4
[155] fitdistrplus_1.1-3 BiocParallel_1.24.1
[157] bit64_4.0.5 foreach_1.5.1
[159] spatstat.core_2.0-0 combinat_0.0-8
[161] cytolib_2.2.1 rsvd_1.0.5
[163] devtools_2.4.0 VGAM_1.1-5
[165] memoise_2.0.0 rio_0.5.26
[167] geneplotter_1.68.0 callr_3.6.0
[169] caret_6.0-86 ps_1.6.0
[171] curl_4.3 fansi_0.4.2
[173] GSEABase_1.52.1 tensor_1.5
[175] edgeR_3.32.1 checkmate_2.0.0
[177] cachem_1.0.4 desc_1.3.0
[179] deldir_0.2-10 rjson_0.2.20
[181] openxlsx_4.2.3 rstatix_0.7.0
[183] clue_0.3-59 rprojroot_2.0.2
[185] tools_4.0.5 magrittr_2.0.1
[187] RCurl_1.98-1.3 proxy_0.4-25
[189] car_3.0-10 xml2_1.3.2
[191] httr_1.4.2 assertthat_0.2.1
[193] globals_0.14.0 R6_2.5.0
[195] Rhdf5lib_1.12.1 nnet_7.3-16
[197] genefilter_1.72.1 gtools_3.8.2
[199] shape_1.4.5 statmod_1.4.35
[201] beachmat_2.6.4 cydar_1.15.1
[203] HDF5Array_1.18.1 BiocSingular_1.6.0
[205] rhdf5_2.34.0 splines_4.0.5
[207] AUCell_1.12.0 carData_3.0-4
[209] colorspace_2.0-0 generics_0.1.0
[211] base64enc_0.1-3 gridtext_0.1.4
[213] pillar_1.6.2 tweenr_1.0.2
[215] HSMMSingleCell_1.10.0 RcppXPtrUtils_0.1.1
[217] GenomeInfoDbData_1.2.4 plyr_1.8.6
[219] gtable_0.3.0 rvest_1.0.0
[221] zip_2.1.1 monocle_2.18.0
[223] knitr_1.32 latticeExtra_0.6-29
[225] fastmap_1.1.0 Cairo_1.5-12.2
[227] AnnotationDbi_1.52.0 broom_0.7.6
[229] scales_1.1.1 backports_1.2.1
[231] writexl_1.3.1 densityClust_0.3
[233] ipred_0.9-11 hms_1.0.0
[235] ggforce_0.3.3 Rtsne_0.15
[237] shiny_1.6.0 dyngen_1.0.1
[239] KMsurv_0.1-5 polyclip_1.10-0
[241] lazyeval_0.2.2 Formula_1.2-4
[243] crayon_1.4.1 MASS_7.3-54
[245] pROC_1.17.0.1 sparseMatrixStats_1.2.1
[247] viridis_0.6.0 rpart_4.1-15
[249] compiler_4.0.5 ggtext_0.1.1
[251] spatstat.geom_2.1-0`