testing more comprehensive quick figure reconstruction

decode_analysis/README.md

@@ -10,11 +10,15 @@ of the analysis can be generated by running the blast-based mapping
 pipeline in [`run_blast.sh`](run_blast.sh) and the analysis pipeline
 in [`run_analysis.sh`](run_analysis.sh).
 
-If you are only interested in the downstream analysis and generation
-of all published figures you just need to download the data (step 3),
-and can directly use the R scripts called from
+**Figures only:** If you are only interested in the downstream
+analysis and generation of all published figures you just need to
+[download the
+data](ttps://drive.google.com/file/d/1uMiGDFmludOoBQpHWGX9CmXac2muMfKF/view?usp=drive_link)
+(step 3 below), and can directly use the R scripts called from
 [`run_analysis.sh`](run_analysis.sh) (step 5) in in your favorite R
-environment.
+environment; simply adjust the `proj.path` variable in
+[`raas_init.R`](raas_init.R), the directory where you unpacked
+`additionalData.zip`.
 
 To seamlessly run all scripts you need to follow these steps:
 
@@ -84,7 +88,7 @@ performance computing, we provide `saap_mapped.tsv` with the
 If you do want to re-run the full pipeline, you need to generate this
 input data **or** modify the R script
 [`map_peptides.R`](map_peptides.R), and the downstream analysis
-scripts to not use all data. Many analyses do not require all data. To
+scripts to not use all data. Many analyses **do not require all data**. To
 use a freshly generated `saap_mapped.tsv` in downstream analyses (next
 step), you need to copy it from the processedData to the
 additionalData folder, overwriting the downloaded original, or adjust