Figures for manuscript
Will Macnair
Institute for Molecular Life Sciences, University of Zurich, SwitzerlandSwiss Institute of Bioinformatics (SIB), University of Zurich, SwitzerlandDecember 17, 2021
Last updated: 2021-12-17
Checks: 4 3
Knit directory: MS_lesions/
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- dotplot_marker_genes
- module_go_terms_annotations
- module_scores_opc_oligo
- plot_dotplot_dheeraj_compact
- plot_test
- plot_umap_all_celltypes
- plot_umap_final_celltypes_sel
- plot_umap_opc_oligo_only
- save_outputs
- session_info
- session-info-chunk-inserted-by-workflowr
- umap_all_celltypes
- umap_opc_oligo
To ensure reproducibility of the results, delete the cache directory ms00_manuscript_figures_cache and re-run the analysis. To have workflowr automatically delete the cache directory prior to building the file, set delete_cache = TRUE when running wflow_build() or wflow_publish().
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Ignored files:
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Unstaged changes:
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Modified: code/supp10_muscat.R
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There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.
Setup / definitions
Libraries
Helper functions
source('code/ms00_utils.R')
library("knitr")Figure 1
B-1
UMAP of all celltypes
include_graphics("figure/ms12_markers.Rmd/plot_umap_final_celltypes_sel-1.png", error = FALSE)
| Version | Author | Date |
|---|---|---|
| 7fb1b95 | wmacnair | 2021-11-25 |
B-2
Dotplot of selected marker genes
include_graphics("figure/ms12_markers.Rmd/plot_dotplot_dheeraj_compact-1.png", error = FALSE)
| Version | Author | Date |
|---|---|---|
| 7fb1b95 | wmacnair | 2021-11-25 |
C-1
UMAP of just OPCs and oligos
include_graphics("figure/ms12_markers.Rmd/plot_umap_opc_oligo_only-1.png", error = FALSE)
| Version | Author | Date |
|---|---|---|
| 7fb1b95 | wmacnair | 2021-11-25 |
C-2
Module scores for OPCs and oligos
include_graphics("figure/ms08_modules.Rmd/plot_scores_by_type_scaled-1.png", error = FALSE)
C-3
GO term annotations for OPC and oligo modules
include_graphics("figure/ms08_modules.Rmd/plot_annotations_std-1.png", error = FALSE)
Outputs
devtools::session_info()- Session info ---------------------------------------------------------------
setting value
version R version 4.0.5 (2021-03-31)
os CentOS Linux 7 (Core)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype C
tz Europe/Zurich
date 2021-12-17
- Packages -------------------------------------------------------------------
package * version date lib source
assertthat * 0.2.1 2019-03-21 [2] CRAN (R 4.0.0)
BiocManager 1.30.16 2021-06-15 [1] CRAN (R 4.0.3)
BiocStyle * 2.18.1 2020-11-24 [1] Bioconductor
bslib 0.3.1 2021-10-06 [2] CRAN (R 4.0.5)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.0.5)
callr 3.7.0 2021-04-20 [2] CRAN (R 4.0.3)
cellranger 1.1.0 2016-07-27 [2] CRAN (R 4.0.0)
circlize * 0.4.13 2021-06-09 [1] CRAN (R 4.0.3)
cli 3.0.1 2021-07-17 [1] CRAN (R 4.0.3)
codetools 0.2-18 2020-11-04 [2] CRAN (R 4.0.3)
colorout * 1.2-2 2021-04-15 [1] Github (jalvesaq/colorout@79931fd)
colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.0.3)
crayon 1.4.1 2021-02-08 [2] CRAN (R 4.0.3)
data.table * 1.14.2 2021-09-27 [2] CRAN (R 4.0.5)
DBI 1.1.1 2021-01-15 [2] CRAN (R 4.0.3)
desc 1.4.0 2021-09-28 [1] CRAN (R 4.0.5)
devtools 2.4.2 2021-06-07 [1] CRAN (R 4.0.3)
digest 0.6.28 2021-09-23 [2] CRAN (R 4.0.5)
dplyr 1.0.7 2021-06-18 [2] CRAN (R 4.0.3)
ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.0.3)
evaluate 0.14 2019-05-28 [2] CRAN (R 4.0.0)
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[1] /pstore/home/macnairw/lib/conda_r3.12
[2] /pstore/home/macnairw/.conda/envs/r_4.0.3/lib/R/library
sessionInfo()R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /pstore/home/macnairw/.conda/envs/r_4.0.3/lib/libopenblasp-r0.3.12.so
locale:
[1] LC_CTYPE=C 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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] knitr_1.36 readxl_1.3.1 forcats_0.5.1 ggplot2_3.3.5
[5] scales_1.1.1 viridis_0.6.2 viridisLite_0.4.0 assertthat_0.2.1
[9] stringr_1.4.0 data.table_1.14.2 magrittr_2.0.1 circlize_0.4.13
[13] RColorBrewer_1.1-2 BiocStyle_2.18.1 colorout_1.2-2 workflowr_1.6.2
loaded via a namespace (and not attached):
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[4] rprojroot_2.0.2 digest_0.6.28 utf8_1.2.2
[7] R6_2.5.1 cellranger_1.1.0 evaluate_0.14
[10] highr_0.9 pillar_1.6.4 GlobalOptions_0.1.2
[13] rlang_0.4.12 callr_3.7.0 jquerylib_0.1.4
[16] rmarkdown_2.11 desc_1.4.0 devtools_2.4.2
[19] munsell_0.5.0 compiler_4.0.5 httpuv_1.6.3
[22] xfun_0.27 pkgconfig_2.0.3 pkgbuild_1.2.0
[25] shape_1.4.6 htmltools_0.5.2 tidyselect_1.1.1
[28] tibble_3.1.5 gridExtra_2.3 codetools_0.2-18
[31] fansi_0.5.0 crayon_1.4.1 dplyr_1.0.7
[34] withr_2.4.2 later_1.3.0 grid_4.0.5
[37] jsonlite_1.7.2 gtable_0.3.0 lifecycle_1.0.1
[40] DBI_1.1.1 git2r_0.28.0 cli_3.0.1
[43] stringi_1.7.4 cachem_1.0.6 remotes_2.4.1
[46] fs_1.5.0 promises_1.2.0.1 testthat_3.1.0
[49] bslib_0.3.1 ellipsis_0.3.2 generics_0.1.1
[52] vctrs_0.3.8 tools_4.0.5 glue_1.4.2
[55] purrr_0.3.4 pkgload_1.2.3 processx_3.5.2
[58] fastmap_1.1.0 yaml_2.2.1 colorspace_2.0-2
[61] BiocManager_1.30.16 sessioninfo_1.1.1 memoise_2.0.0
[64] usethis_2.1.2 sass_0.4.0