complete figure references for rscript calls in run_analaysis.sh

decode_analysis/run_analysis.sh

@@ -7,6 +7,7 @@ if ! command -v R &> /dev/null; then
     exit 1
 fi
 
+
 ## Note, that all scripts also load functions defined in
 ## raas_utils.R
 
@@ -19,13 +20,13 @@ fi
 R --vanilla <  raas_init.R &> $DECODE/log/raas_init.txt  
 
 ### CALCULATE RAAS PROFILES and GENERATE PUBLICATION FIGURES
-R --vanilla < codons.R &> $DECODE/log/codons.txt  # FIGURE 2
-R --vanilla < aminoacids.R &> $DECODE/log/aminoacids.txt  # FIGURE 3
-R --vanilla < motifs.R &> $DECODE/log/motifs.txt  # FIGURE 4, FIGURE 5
-R --vanilla < function.R &> $DECODE/log/function.txt # FIGURE 4
-R --vanilla < kraq.R &> $DECODE/log/kraq.txt  # Ext. Data Figure 8: motifs
-R --vanilla < proteins.R &> $DECODE/log/proteins.txt # FIGURE 5
-R --vanilla < structure.R &> $DECODE/log/structure.txt  # Ext. Data Figure 10
-R --vanilla < rna.R &> $DECODE/log/rna.txt # Suppl. Figure 2
+R --vanilla < codons.R &> $DECODE/log/codons.txt  # Fig. 2j, EFig. 3k, 4
+R --vanilla < aminoacids.R &> $DECODE/log/aminoacids.txt  # Fig. 3b,c,e, EFig. 5a,c,f
+R --vanilla < function.R &> $DECODE/log/function.txt # Fig. 4c, EFig. 7
+R --vanilla < motifs.R &> $DECODE/log/motifs.txt  # Fig. 4c,d, Fig. 5c, EFig. 8a,c
+R --vanilla < kraq.R &> $DECODE/log/kraq.txt  # EFig. 8b
+R --vanilla < proteins.R &> $DECODE/log/proteins.txt # Fig. 5a,b, EFig. 10a
+R --vanilla < structure.R &> $DECODE/log/structure.txt  # EFig. 10b,c
+R --vanilla < rna.R &> $DECODE/log/rna.txt # SFig. 2
 
 ## TODO: add 1d protein plots and chimeraX generating code