Add fig1 summary to README (#649)

* Add figure 1 summary to `README` file

- change script to generate a png figure instead of pdf figure to be consistent with the other figures in `pngs` directory and for linking purposes to the manuscript

* remove pdf figure

* update comment

* add more detail to notes field in fig1 summary

figures/README.md

@@ -40,6 +40,7 @@ However, we list information about the resources, intermediate steps, and [PBTA
 
 | Figure | Individual script | Notes on requirements | Linked analysis modules | PBTA data files consumed |
 |--------|--------|------------------|-------------------------|-----------------------------|
+| Figure 1 | [scripts/fig1-sample-distribution.R`](./scripts/fig1-sample-distribution.R) | No high RAM requirements | [`sample-distribution-analysis`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/sample-distribution-analysis) |  `pbta-histologies.tsv` |
 | Figure 2 | [scripts/fig2-mutational-landscape.R`](./scripts/fig2-mutational-landscape.R) | ~128MB of RAM are needed due to the run_caller_consensus_analysis-pbta.sh handling of large MAF files|[`snv-callers`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/snv-callers) <br> [`mutational-signatures`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/mutational-signatures) |  `pbta-snv-lancet.vep.maf.gz` <br> `pbta-snv-mutect2.vep.maf.gz` <br> `pbta-snv-strelka2.vep.maf.gz` <br> `pbta-snv-vardict.vep.maf.gz` <br> `tcga-snv-lancet.vep.maf.gz` <br> `tcga-snv-mutect2.vep.maf.gz` <br> `tcga-snv-strelka2.vep.maf.gz` |
 
 ## Color Palette Usage

figures/scripts/fig1-sample-distribution.R

@@ -124,8 +124,8 @@ combined_plot <- treemap + project_features_plot +
     axis.text.x = element_text(size = 9),
     axis.text.y = element_text(size = 9))
 
-# Save to PDF
-ggplot2::ggsave(file.path(output_dir, "fig1-openpbta-distribution.pdf"),
+# Save to PNG
+ggplot2::ggsave(file.path(output_dir, "fig1-openpbta-distribution.png"),
                 width = 12, height = 8,
                 units = "in"
 )