Figures for manuscript
Will Macnair
Institute for Molecular Life Sciences, University of Zurich, SwitzerlandSwiss Institute of Bioinformatics (SIB), University of Zurich, SwitzerlandDecember 20, 2021
Last updated: 2021-12-20
Checks: 4 3
Knit directory: MS_lesions/
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- ancom_bootstrapped_gm_4pcs
- ancom_bootstrapped_gm
- ancom_bootstrapped_wm
- dotplot_marker_genes
- effect_of_including_pcs_neurons
- effect_of_including_pcs_others
- fixed_vs_random_gm_4pcs
- fixed_vs_random_gm
- fixed_vs_random_wm
- gm_vs_wm_proportions
- grp17_cell_abundances
- module_go_terms_annotations
- module_scores_opc_oligo
- oligo_barplot_gm
- oligo_barplot_wm
- 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
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 1a38d84 | wmacnair | 2021-12-17 | Add initial version of file with all figures |
| html | 1a38d84 | wmacnair | 2021-12-17 | Add initial version of file with all figures |
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)
Figure 2
A
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)
B
WM oligodendroglia proportions barplot
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_sample_splits_bars_oligos-1.png", error = FALSE)
C
Differential abundance results for WM
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_bootstraps_lesions-1.png", error = FALSE)
D
Comparison of Sarah’s validation of GPR17-expressing cells
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_no_gpr17_cells-1.png", error = FALSE)
Figure 4
A
Illustration of random effects model
include_graphics("figure/ms15_mofa_sample_wm_final_meta.Rmd/fig_random_effects_example-3.png", error = FALSE)
| Version | Author | Date |
|---|---|---|
| 7fb1b95 | wmacnair | 2021-11-25 |
B
Disease effect vs donor effect
include_graphics("figure/ms15_mofa_sample_wm_final_meta.Rmd/plot_muscat_vs_sd_min-3.png", error = FALSE)
C
MOFA factors
include_graphics("figure/ms15_mofa_sample_wm_final_meta.Rmd/fig_mofa_factors_diagnosis-1.png", error = FALSE)
| Version | Author | Date |
|---|---|---|
| 7fb1b95 | wmacnair | 2021-11-25 |
D
Variance explained
include_graphics("figure/ms15_mofa_sample_wm_final_meta.Rmd/fig_factor_r2s-1.png", error = FALSE)
| Version | Author | Date |
|---|---|---|
| 7fb1b95 | wmacnair | 2021-11-25 |
E
Patient stratification
include_graphics("figure/ms15_mofa_sample_wm_final_meta.Rmd/fig_f1_vs_f2-3.png", error = FALSE)
| Version | Author | Date |
|---|---|---|
| 7fb1b95 | wmacnair | 2021-11-25 |
F
Factor 1 top genes
include_graphics("figure/ms15_mofa_sample_wm_final_meta.Rmd/fig_factor1-1.png", error = FALSE)
| Version | Author | Date |
|---|---|---|
| 7fb1b95 | wmacnair | 2021-11-25 |
G
Factor 2 top genes
include_graphics("figure/ms15_mofa_sample_wm_final_meta.Rmd/fig_factor2-1.png", error = FALSE)
| Version | Author | Date |
|---|---|---|
| 7fb1b95 | wmacnair | 2021-11-25 |
Supplementary figures
S1
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)
S2
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)
S3
DA results for GM, no layers
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_bootstraps_lesions-2.png", error = FALSE)
S4
DA results for GM, 4 layer PCs
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_bootstraps_lesions-6.png", error = FALSE)
S5
Effect of including PCs, neurons
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_effect_of_pcs_lesions-1.png", error = FALSE)
S6
Effect of including PCs, other celltypes
include_graphics("figure/ms09_ancombc_mixed.Rmd/plot_effect_of_pcs_lesions-2.png", error = FALSE)
End
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setting value
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Platform: x86_64-conda-linux-gnu (64-bit)
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