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Knit directory: MS_lesions/
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File | Version | Author | Date | Message |
---|---|---|---|---|
Rmd | fea6733 | wmacnair | 2022-01-27 | Update location of manuscript figures |
html | fea6733 | wmacnair | 2022-01-27 | Update location of manuscript figures |
source('code/ms00_utils.R')
library("knitr")
UMAP
applied to subset of 100k cells (subset because of memory limits), using parameters min_dist = 1, spread = 2
, otherwise defaults. Clusters are determined by Louvain clustering applied to the conos
graph, followed by post-hoc splitting of two clusters based on biological expectations (COPs and immune cells), and merging of very similar clusters (using SCCAF
).
include_graphics("figure/ms12_markers.Rmd/plot_umap_final_celltypes_sel-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
7fb1b95 | wmacnair | 2021-11-25 |
UMAP
plot as in B-1, restricted to just oligodendrocyte and OPC celltypes.
include_graphics("figure/ms12_markers.Rmd/plot_umap_opc_oligo_only-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
7fb1b95 | wmacnair | 2021-11-25 |
Median oNMF
module score per fine celltype for OPC and oligo modules and cells. Columns are scaled to have max value equal to 1.
include_graphics("figure/ms08_modules.Rmd/plot_scores_by_type_scaled-1.png", error = FALSE)
Expression of top genes for each oligo-OPC module (gene selected if weight >2%). Expression calculated across all cells and samples.
include_graphics("figure/ms08_modules.Rmd/plot_genes_dotplot-2.png", error = FALSE)
Proportions of fine celltypes in healthy GM and healthy WM. Neuronal celltypes excluded. Negative binomial model fit to absolute numbers for each celltype, using total number of cells in sample as offset. FDR calculated across all celltypes.
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_wm_vs_gm-1.png", error = FALSE)
Contribution to variability in celltype abundances explained by lesion + patient in WM.
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_lrt_results-1.png", error = FALSE)
Contribution to variability in celltype abundances explained by lesion + patient in GM, no layers.
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_lrt_results-2.png", error = FALSE)
Differential abundance results for WM.
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_bootstraps_lesions_signif-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
270e5fc | wmacnair | 2021-11-26 |
Differential abundance results for GM (with layers factored out).
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_bootstraps_lesions_signif-6.png", error = FALSE)
Version | Author | Date |
---|---|---|
270e5fc | wmacnair | 2021-11-26 |
include_graphics("figure/ms99_deg_figures_gm.Rmd/plot_de_barplot_sel-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
d83826d | wmacnair | 2022-01-27 |
include_graphics("figure/ms99_deg_figures_wm.Rmd/plot_de_barplot_sel-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
d83826d | wmacnair | 2022-01-27 |
Dotplot of Hallmark module results for GM.
[IN PRODUCTION]
Dotplot of Hallmark module results for WM.
[IN PRODUCTION]
Heatmap of selected interferon genes.
[IN PRODUCTION]
Genetic enrichment of differentially expressed genes.
include_graphics("figure/gwas_figures/de_barplots.png", error = FALSE)
Version | Author | Date |
---|---|---|
b1e52a7 | wmacnair | 2022-01-06 |
Clustering of WM fold change profiles. Restricted to genes where at least one lesion type has FDR < 5%. Clusters split so that average logFC difference between clusters is > log(4); clusters with fewer than 5 genes not shown; clusters ordered in descending order of mean logFC.
include_graphics("figure/ms99_deg_figures_wm.Rmd/plot_fc_cluster_profiles-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
d83826d | wmacnair | 2022-01-27 |
Clustered expression heatmap of WM genes.
include_graphics("figure/ms15_mofa_sample_wm_final_meta_bigger.Rmd/fig_overview_expression-2.png", error = FALSE)
Version | Author | Date |
---|---|---|
8bc5188 | wmacnair | 2022-01-27 |
Variance explained
include_graphics("figure/ms15_mofa_sample_wm_final_meta_bigger.Rmd/fig_factor_r2s-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
8bc5188 | wmacnair | 2022-01-27 |
First two PCs of CLRs of oligodendroglia proportions.
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_sample_splits_clrs_oligos-6.png", error = FALSE)
Version | Author | Date |
---|---|---|
8364a6f | wmacnair | 2021-12-13 |
Patient stratification via MOFA factors.
include_graphics("figure/ms15_mofa_sample_wm_final_meta_bigger.Rmd/plot_factors_heatmap_few-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
8bc5188 | wmacnair | 2022-01-27 |
Factor 1 top genes
include_graphics("figure/ms15_mofa_sample_wm_final_meta_bigger.Rmd/fig_factor1-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
8bc5188 | wmacnair | 2022-01-27 |
Factor 3 top genes
include_graphics("figure/ms15_mofa_sample_wm_final_meta_bigger.Rmd/fig_factor3-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
8bc5188 | wmacnair | 2022-01-27 |
Factor 5 top genes
include_graphics("figure/ms15_mofa_sample_wm_final_meta_bigger.Rmd/fig_factor5-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
8bc5188 | wmacnair | 2022-01-27 |
Post-QC summary of samples
include_graphics("de_reports/figure/ms03_SampleQC.Rmd/plot_totals_split_by_meta-1.png", error = FALSE)
[SCCAF]
include_graphics("de_reports/figure/ms03_SampleQC.Rmd/plot_totals_split_by_meta-1.png", error = FALSE)
Expression of marker genes selected for broad celltypes, and for fine celltypes. Expression calculated across all cells and samples.
include_graphics("figure/ms12_markers.Rmd/plot_dotplot_dheeraj_compact-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
7fb1b95 | wmacnair | 2021-11-25 |
[Cluster mixing]
include_graphics("figure/ms04_conos.Rmd/plot_conos_mixing-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
7fb1b95 | wmacnair | 2021-11-25 |
[GM layer effects]
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_propns_layers-1.png", error = FALSE)
WM oligodendroglia proportions barplot
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_sample_splits_bars_oligos-1.png", error = FALSE)
Comparison of Sarah’s validation of GPR17-expressing cells
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_no_gpr17_cells-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
afba18d | wmacnair | 2021-12-20 |
Contribution to variability in celltype abundances explained by lesion + patient in GM, including 4 layer PCs
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_lrt_results-6.png", error = FALSE)
DA results for GM, no layers
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_bootstraps_lesions-2.png", error = FALSE)
include_graphics("figure/ms99_deg_figures_wm.Rmd/plot_causes_of_variability-1.png", error = FALSE)
include_graphics("figure/ms99_deg_figures_gm.Rmd/plot_causes_of_variability-1.png", error = FALSE)
include_graphics("figure/ms15_mofa_sample_gm_w_layers_final_meta.Rmd/fig_overview_expression-2.png", error = FALSE)
Version | Author | Date |
---|---|---|
1d0d7e8 | wmacnair | 2022-01-21 |
Effect of including PCs, neurons
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_effect_of_pcs_lesions-1.png", error = FALSE)
Effect of including PCs, other celltypes
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_effect_of_pcs_lesions-2.png", error = FALSE)
GM oligodendroglia proportions barplot
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_sample_splits_bars_oligos-2.png", error = FALSE)
Illustration of random effects model
include_graphics("figure/ms15_mofa_sample_wm_final_meta_bigger.Rmd/fig_random_effects_example-3.png", error = FALSE)
Version | Author | Date |
---|---|---|
8bc5188 | wmacnair | 2022-01-27 |
Disease effect vs donor effect
include_graphics("figure/ms15_mofa_sample_wm_final_meta_bigger.Rmd/fig_muscat_vs_sd-1.png", error = FALSE)
MOFA factors
include_graphics("figure/ms15_mofa_sample_wm_final_meta_bigger.Rmd/fig_mofa_factors_diagnosis-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
8bc5188 | wmacnair | 2022-01-27 |
Manhattan plot of MAGMA differentially expressed genes
include_graphics("figure/gwas_figures/manhattan.png", error = FALSE)
Version | Author | Date |
---|---|---|
b1e52a7 | wmacnair | 2022-01-06 |
Example of a coloc gene that is differentially expressed
include_graphics("figure/gwas_figures/coloc_example_gene_NR1H3_microglia.png", error = FALSE)
Version | Author | Date |
---|---|---|
b1e52a7 | wmacnair | 2022-01-06 |
Expression heatmap of WM genes, ordered by lesion type.
include_graphics("figure/ms15_mofa_sample_wm_final_meta_bigger.Rmd/fig_overview_expression-4.png", error = FALSE)
Version | Author | Date |
---|---|---|
8bc5188 | wmacnair | 2022-01-27 |
Patient stratification
include_graphics("figure/ms15_mofa_sample_wm_final_meta_bigger.Rmd/fig_f1_vs_f2-3.png", error = FALSE)
Version | Author | Date |
---|---|---|
8bc5188 | wmacnair | 2022-01-27 |
devtools::session_info()
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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 2022-01-28
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[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):
[1] Rcpp_1.0.7 prettyunits_1.1.1 ps_1.6.0
[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 whisker_0.4
[16] jquerylib_0.1.4 rmarkdown_2.11 desc_1.4.0
[19] devtools_2.4.2 munsell_0.5.0 compiler_4.0.5
[22] httpuv_1.6.3 xfun_0.27 pkgconfig_2.0.3
[25] pkgbuild_1.2.0 shape_1.4.6 htmltools_0.5.2
[28] tidyselect_1.1.1 tibble_3.1.5 gridExtra_2.3
[31] codetools_0.2-18 fansi_0.5.0 crayon_1.4.1
[34] dplyr_1.0.7 withr_2.4.2 later_1.3.0
[37] grid_4.0.5 jsonlite_1.7.2 gtable_0.3.0
[40] lifecycle_1.0.1 DBI_1.1.1 git2r_0.28.0
[43] cli_3.0.1 stringi_1.7.4 cachem_1.0.6
[46] remotes_2.4.1 fs_1.5.0 promises_1.2.0.1
[49] testthat_3.1.0 bslib_0.3.1 ellipsis_0.3.2
[52] generics_0.1.1 vctrs_0.3.8 tools_4.0.5
[55] glue_1.4.2 purrr_0.3.4 pkgload_1.2.3
[58] processx_3.5.2 fastmap_1.1.0 yaml_2.2.1
[61] colorspace_2.0-2 BiocManager_1.30.16 sessioninfo_1.1.1
[64] memoise_2.0.0 usethis_2.1.2 sass_0.4.0