Scripts exclusively for publication-ready plots
We list information about the relevant figures and modules for each script in this directory below for convenience.
| Individual script |
Figure(s) |
Linked analysis modules |
fig1-sample-distribution.R |
Figure 1B |
N/A |
fig2_figS3-oncoprint-landscape.R |
Figure 2 & Figure S3B |
oncoprint-landscape |
fig3-chromothripsis-barplot.R |
Figure 3D |
chromothripsis |
fig3_figS4-mutational-signatures-panels.R |
Figure 3E and Figure S4 |
mutational-signatures |
fig4-tp53-telomerase-panels.R |
Figure 4 panels A, B, C, D, F |
tp53_nf1_score
telomerase-activity-prediction
survival-analysis |
fig4-heatmap.R |
Figure 4E |
mutational-signatures |
fig4-hgg-kaplan-meier.R |
Figure 4H |
survival-analysis |
fig4-hgg-subtype-forest-plot.R |
Figure 4G |
survival-analysis |
fig5-panels-gsva-umap.R |
Figure 5 panels A, B |
transcriptomic-dimension-reduction
collapse-rnaseq
gene-set-enrichment-analysis |
fig5-forest-plot.R |
Figure 5D |
survival-analysis
immune-deconv |
fig5_figS6-immune-deconv-panels.R |
Figure 5 panels C, E and Figure S6 panels E, F |
immune-deconv |
figS2-snv-callers-panels.R |
Figure S2 panels A-G |
snv-callers (:warning: Requires 32 GB RAM) |
figS2-tmb-compare-panels.R |
Figure S2 panels H, I |
tmb-compare |
figS3-panels-cn-chromothripsis.R |
Figure S3 panels C, D, E |
cnv-chrom-plot
chromothripsis
copy_number_consensus_call |
figS5-all-panels.R |
Figure S5 A-C |
tp53_nf1_score
telomerase-activity-prediction |
figS6-subtype-umap-panels.R |
Figure S6 panels A-D |
transcriptomic-dimension-reduction |
figS7-seqcenter-barplot.R |
Figure S7 panel A |
None |
figS7-UMAP-libraries.R |
Figure S7 panel B |
None |
figS7-tp53-telomerase-tumor-purity-threshold.R |
Figure S7 panel G |
transcriptomic-dimension-reduction
telomerase-activity-prediction
tumor-purity-exploration |