Last updated: 2022-02-03
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Knit directory: MS_lesions/
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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, including 4 layer PCs.
# include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_lrt_results-2.png", error = FALSE)
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_lrt_results-6.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)
[TO DO: summaries of post-QC QC metrics]
[TO UPDATE: cluster mixing; need to update to merged version]
include_graphics("figure/ms04_conos.Rmd/plot_conos_mixing-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
7fb1b95 | wmacnair | 2021-11-25 |
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 |
[Eneritz to provide: comparing oligo cell types in this paper and previous nature paper]
[TO DO: astrocyte module genes]
Proportions of neuronal compartment per sample, split by layer-specificity of neurons. L1 and L2/L3 neurons account for relatively low proportions of NAGM samples, while L5 and L6 neurons account for high proportions of NAGM samples; vice versa for GML samples, while ctrl GM lies in the middle. This indicates that, on average, the samples are roughly ordered as follows: NAGM is deeper than ctrl GM, which is deeper than GML.
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_propns_layers-1.png", error = FALSE)
Principal components of GM neuronal layer centred log ratios (CLRs; see Methods). y-axis shows absolute Spearman correlation between PC loadings and neuronal layer numbers (excluding neuronal clusters without an assigned layer number). x-axis shows the variance explained by each PC (on a log scale). Dashed lines show thresholds at 0.2 Spearman correlation, and 1% variance explained, giving up to 7 PCs that could be relevant to layers.
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_layer_var_exp-1.png", error = FALSE)
Bootstrapped ANCOM-BC results including varying numbers of PCs as covariates. Number of PCs used varies from 0 to 7 (see S4B for rationale for 7). Grey lines show 95% bootstrapped confidence interval, coloured lines show 80% confidence interval; based on 20k bootstraps (large number taken to give reliable estimates of tails; see [ref: Hesterberg 2011]).
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_effect_of_pcs_lesions-1.png", error = FALSE)
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_effect_of_pcs_lesions-2.png", error = FALSE)
Proportions of all non-contaminated genes with MS effect and / or donor effect, in WM. MS effect defined as: FDR < 1% for at least one lesion type, and abs(logFC) > log(1.5) (i.e. expression change of +/-50%). Donor effect defined as: ANOVA for inclusion of random effect in model has FDR < 1%, and SD(random effects) > log(1.5).
include_graphics("figure/ms99_deg_figures_wm.Rmd/plot_causes_of_variability-1.png", error = FALSE)
Proportions of all non-contaminated genes with MS effect and / or donor effect, in GM. MS effect defined as: FDR < 1% for at least one lesion type, and abs(logFC) > log(1.5) (i.e. expression change of +/-50%). Donor effect defined as: ANOVA for inclusion of random effect in model has FDR < 1%, and SD(random effects) > log(1.5).
include_graphics("figure/ms99_deg_figures_gm.Rmd/plot_causes_of_variability-1.png", error = FALSE)
[IN PRODUCTION: DEG barplots for fine celltypes]
[IN PRODUCTION: dot plot of GM fine type GO terms]
[IN PRODUCTION: heatmap of selected genes in GM: GRIA1, GRIA2, GRIA4, GRIN2B, GRM1, GRM5, SLC2A12, SLC22A10, SCN1A, SCN1B, SCN2B, SCN4B, KCNA1, KCNA2, KCNC1, OXPHOS, ATP1A1, ATP1B1, NDUFB10, NDUFS3, UQCRH]
[barplot of DEGs in fine cell types]
Distribution of model fits for genes for each broad celltype in WM. y-axis shows standard deviation of random (donor) effects for each gene. x-axis shows log2FC of lesion type with smallest p-value for each gene. Horizontal dashed lines show cutoff at SD = log(1.5); vertical dashed lines show cutoff at abs(log2FC) = log(1.5).
include_graphics("figure/ms15_mofa_sample_wm_final_meta_bigger.Rmd/fig_interesting_gs-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
8bc5188 | wmacnair | 2022-01-27 |
Distribution of model fits for genes for each broad celltype in GM. y-axis shows standard deviation of random (donor) effects for each gene. x-axis shows log2FC of lesion type with smallest p-value for each gene. Horizontal dashed lines show cutoff at SD = log(1.5); vertical dashed lines show cutoff at abs(log2FC) = log(1.5).
include_graphics("figure/ms15_mofa_sample_gm_w_layers_final_meta.Rmd/fig_interesting_gs-1.png", error = FALSE)
Version | Author | Date |
---|---|---|
1d0d7e8 | wmacnair | 2022-01-21 |
[show absence of WM oligo pattern in GM: maybe take WM PCs, apply to GM?]
[MOFA cartoon]
[CLARIFYING: maybe same as S8A? see comment in manuscript]
Distributions of MOFA factors. Colour denotes donor; grey is used where only one sample was obtained from a donor.
include_graphics("figure/ms15_mofa_sample_gm_w_layers_final_meta.Rmd/fig_mofa_factors_lesions-1.png", error = FALSE)
First panel shows variation in expression for each celltype explained by MOFA+ factors; second panel shows extent to which MOFA+ factors can be accounted for by metadata. Variance explained in first panel is per celltype, so the maximum total for each row is 100%. Pseudo-R2 values are calculated by fitting a mixed model to each factor, using model factor_value ~ lesion_type + sex + age_scale + pmi_cat + (1 | donor_id), and the glmmTMB
function in package glmmTMB
. Pseudo-R2 values are determined by Nakagawa’s R2, showing proportion of variance explained using fixed components only, and including a donor effect (see Methods).
include_graphics("figure/ms15_mofa_sample_gm_w_layers_final_meta.Rmd/fig_factor_r2s-1.png", error = FALSE)
[IN PRODUCTION: plot extent of overlap between factor genes in WM]
[CLARIFYING: see comment in manuscript]
[DEGs for each broad cell type (fdr <0.01 & log FC > 1.5) with same annotation (specific to cell types, shared between lesions within a cell type and shared between cell types)]
[MAGMA MS genes (fdr < 0.05) which are DEGs in pericytes, endo and opc/cops]
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 |
DA results for GM, no layers
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_bootstraps_lesions-2.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 |
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 |
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()
- 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 2022-01-28
- Packages -------------------------------------------------------------------
package * version date lib source
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prettyunits 1.1.1 2020-01-24 [2] CRAN (R 4.0.0)
processx 3.5.2 2021-04-30 [2] CRAN (R 4.0.3)
promises 1.2.0.1 2021-02-11 [2] CRAN (R 4.0.3)
ps 1.6.0 2021-02-28 [2] CRAN (R 4.0.3)
purrr 0.3.4 2020-04-17 [2] CRAN (R 4.0.0)
R6 2.5.1 2021-08-19 [2] CRAN (R 4.0.5)
RColorBrewer * 1.1-2 2014-12-07 [2] CRAN (R 4.0.0)
Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.0.3)
readxl * 1.3.1 2019-03-13 [2] CRAN (R 4.0.0)
remotes 2.4.1 2021-09-29 [1] CRAN (R 4.0.5)
rlang 0.4.12 2021-10-18 [2] CRAN (R 4.0.5)
rmarkdown 2.11 2021-09-14 [1] CRAN (R 4.0.5)
rprojroot 2.0.2 2020-11-15 [2] CRAN (R 4.0.3)
sass 0.4.0 2021-05-12 [2] CRAN (R 4.0.3)
scales * 1.1.1 2020-05-11 [2] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.3)
shape 1.4.6 2021-05-19 [1] CRAN (R 4.0.1)
stringi 1.7.4 2021-08-25 [1] CRAN (R 4.0.5)
stringr * 1.4.0 2019-02-10 [2] CRAN (R 4.0.0)
testthat 3.1.0 2021-10-04 [2] CRAN (R 4.0.5)
tibble 3.1.5 2021-09-30 [1] CRAN (R 4.0.5)
tidyselect 1.1.1 2021-04-30 [2] CRAN (R 4.0.3)
usethis 2.1.2 2021-10-25 [1] CRAN (R 4.0.5)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.0.3)
vctrs 0.3.8 2021-04-29 [2] CRAN (R 4.0.3)
viridis * 0.6.2 2021-10-13 [1] CRAN (R 4.0.5)
viridisLite * 0.4.0 2021-04-13 [1] CRAN (R 4.0.1)
whisker 0.4 2019-08-28 [1] CRAN (R 4.0.3)
withr 2.4.2 2021-04-18 [2] CRAN (R 4.0.3)
workflowr * 1.6.2 2020-04-30 [1] CRAN (R 4.0.3)
xfun 0.27 2021-10-18 [1] CRAN (R 4.0.5)
yaml 2.2.1 2020-02-01 [2] CRAN (R 4.0.3)
[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):
[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