Merge pull request #11 from jbloomlab/add_TuGG_and_structural

add delta-expr heatmap with single-nt hashes

collapse_scores.Rmd

@@ -496,6 +496,22 @@ p1 <- ggplot(temp[measurement=="delta_expr" & chain != "link",],aes(position_IMG
 p1
 invisible(dev.print(pdf, paste(config$final_variant_scores_dir,"/heatmap_SSM_delta-expression-by-target.pdf",sep="")))
 ```
+And expression, hatchign out >single-nt-accessible
+
+```{r heatmap_DMS_delta-expression-by-target_singlent, fig.width=30,fig.height=6,fig.align="center", dpi=500,dev="png",echo=T}
+p1 <- ggplot(temp[measurement=="delta_expr" & chain != "link",],aes(position_IMGT,mutant))+geom_tile(aes(fill=value),color="black",lwd=0.1)+
+  scale_fill_gradientn(colours=c("#A94E35","#F48365","#FFFFFF","#7378B9","#383C6C"),limits=c(-4,1),values=c(0/5,2/5,4/5,4.5/5,5/5),na.value="yellow")+
+  #scale_x_continuous(expand=c(0,0),breaks=c(1,seq(5,235,by=5)))+
+  labs(x="",y="")+theme_classic(base_size=9)+
+  coord_equal()+theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.6,face="bold",size=10),axis.text.y=element_text(face="bold",size=10))+
+  guides(y.sec=guide_axis_label_trans())+
+  geom_text(aes(label=wildtype_indicator),size=2,color="gray10")+
+  geom_text(aes(label=multimut_indicator),size=2.5,color="gray10")
+
+p1
+invisible(dev.print(pdf, paste(config$final_variant_scores_dir,"/heatmap_SSM_delta-expression-by-target_singlent.pdf",sep="")))
+```
+
 Make heatmaps faceted by target, showing raw polyspecificity and delta-polyspecificity of muts relative to respective wildtype
 
 ```{r heatmap_DMS_polyspecificity-by-target, fig.width=30,fig.height=6,fig.align="center", dpi=500,dev="png",echo=T}

results/summary/collapse_scores.md

@@ -48,7 +48,7 @@ sessionInfo()
 
     ## R version 3.6.2 (2019-12-12)
     ## Platform: x86_64-pc-linux-gnu (64-bit)
-    ## Running under: Ubuntu 18.04.5 LTS
+    ## Running under: Ubuntu 18.04.4 LTS
     ## 
     ## Matrix products: default
     ## BLAS/LAPACK: /app/software/OpenBLAS/0.3.7-GCC-8.3.0/lib/libopenblas_haswellp-r0.3.7.so
@@ -628,6 +628,27 @@ p1
 invisible(dev.print(pdf, paste(config$final_variant_scores_dir,"/heatmap_SSM_delta-expression-by-target.pdf",sep="")))
 ```
 
+And expression, hatchign out \>single-nt-accessible
+
+``` r
+p1 <- ggplot(temp[measurement=="delta_expr" & chain != "link",],aes(position_IMGT,mutant))+geom_tile(aes(fill=value),color="black",lwd=0.1)+
+  scale_fill_gradientn(colours=c("#A94E35","#F48365","#FFFFFF","#7378B9","#383C6C"),limits=c(-4,1),values=c(0/5,2/5,4/5,4.5/5,5/5),na.value="yellow")+
+  #scale_x_continuous(expand=c(0,0),breaks=c(1,seq(5,235,by=5)))+
+  labs(x="",y="")+theme_classic(base_size=9)+
+  coord_equal()+theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.6,face="bold",size=10),axis.text.y=element_text(face="bold",size=10))+
+  guides(y.sec=guide_axis_label_trans())+
+  geom_text(aes(label=wildtype_indicator),size=2,color="gray10")+
+  geom_text(aes(label=multimut_indicator),size=2.5,color="gray10")
+
+p1
+```
+
+<img src="collapse_scores_files/figure-gfm/heatmap_DMS_delta-expression-by-target_singlent-1.png" style="display: block; margin: auto;" />
+
+``` r
+invisible(dev.print(pdf, paste(config$final_variant_scores_dir,"/heatmap_SSM_delta-expression-by-target_singlent.pdf",sep="")))
+```
+
 Make heatmaps faceted by target, showing raw polyspecificity and
 delta-polyspecificity of muts relative to respective wildtype
 

results/summary/structural_mapping.md

@@ -190,3 +190,41 @@ binding.site(pdb,
     ## [11] "TYR 114 (L)" "PRO 115 (L)" "ASN 38 (C)"  "TYR 55 (C)"  "SER 56 (C)" 
     ## [16] "TYR 66 (C)"  "ARG 67 (C)"  "TYR 68 (C)"  "SER 69 (C)"  "TYR 107 (C)"
     ## [21] "TYR 108 (C)" "SER 109 (C)" "TYR 114 (C)" "PRO 115 (C)"
+
+Below are heavy chain residues that are 5A or closer to light chain in
+each of the two protomers
+
+``` r
+binding.site(pdb,
+             a.inds=atom.select(pdb,chain=c("H","B")),
+             b.inds=atom.select(pdb,chain=c("L","C")),
+             cutoff=5,hydrogens=F)$resnames
+```
+
+    ##  [1] "VAL 2 (H)"   "ASN 40 (H)"  "ILE 42 (H)"  "LYS 44 (H)"  "ASN 48 (H)" 
+    ##  [6] "LEU 50 (H)"  "GLU 51 (H)"  "TYR 52 (H)"  "TYR 55 (H)"  "TYR 66 (H)" 
+    ## [11] "ASN 68 (H)"  "PRO 69 (H)"  "TYR 103 (H)" "ASP 107 (H)" "PHE 115 (H)"
+    ## [16] "ASP 116 (H)" "VAL 117 (H)" "TRP 118 (H)" "GLY 119 (H)" "ALA 120 (H)"
+    ## [21] "ASN 40 (B)"  "ILE 42 (B)"  "LYS 44 (B)"  "ASN 48 (B)"  "LEU 50 (B)" 
+    ## [26] "GLU 51 (B)"  "TYR 52 (B)"  "TYR 55 (B)"  "TYR 66 (B)"  "ASN 68 (B)" 
+    ## [31] "TYR 103 (B)" "ASP 107 (B)" "PHE 115 (B)" "ASP 116 (B)" "TRP 118 (B)"
+    ## [36] "GLY 119 (B)" "ALA 120 (B)"
+
+Below are light chain residues that are 5A or closer to heavy chain in
+each of the two protomers
+
+``` r
+binding.site(pdb,
+             a.inds=atom.select(pdb,chain=c("L","C")),
+             b.inds=atom.select(pdb,chain=c("H","B")),
+             cutoff=5,hydrogens=F)$resnames
+```
+
+    ##  [1] "PHE 42 (L)"  "GLN 44 (L)"  "SER 49 (L)"  "PRO 50 (L)"  "LYS 51 (L)" 
+    ##  [6] "SER 52 (L)"  "TYR 55 (L)"  "TYR 68 (L)"  "GLU 101 (L)" "PHE 103 (L)"
+    ## [11] "HIS 105 (L)" "GLN 106 (L)" "TYR 107 (L)" "TYR 114 (L)" "PRO 115 (L)"
+    ## [16] "LEU 116 (L)" "PHE 118 (L)" "SER 120 (L)" "GLY 121 (L)" "PHE 42 (C)" 
+    ## [21] "GLN 44 (C)"  "GLN 48 (C)"  "SER 49 (C)"  "PRO 50 (C)"  "SER 52 (C)" 
+    ## [26] "TYR 55 (C)"  "GLU 101 (C)" "PHE 103 (C)" "HIS 105 (C)" "GLN 106 (C)"
+    ## [31] "TYR 107 (C)" "TYR 114 (C)" "PRO 115 (C)" "LEU 116 (C)" "PHE 118 (C)"
+    ## [36] "SER 120 (C)" "GLY 121 (C)"

structural_mapping.Rmd

@@ -134,4 +134,24 @@ binding.site(pdb,
              b.inds=atom.select(pdb,chain=c("A","D")),
              cutoff=5,hydrogens=F)$resnames
 
+```
+
+Below are heavy chain residues that are 5A or closer to light chain in each of the two protomers
+
+```{r heavy_contacts_with_light}
+binding.site(pdb,
+             a.inds=atom.select(pdb,chain=c("H","B")),
+             b.inds=atom.select(pdb,chain=c("L","C")),
+             cutoff=5,hydrogens=F)$resnames
+
+```
+
+Below are light chain residues that are 5A or closer to heavy chain in each of the two protomers
+
+```{r light_contacts_with_heavy}
+binding.site(pdb,
+             a.inds=atom.select(pdb,chain=c("L","C")),
+             b.inds=atom.select(pdb,chain=c("H","B")),
+             cutoff=5,hydrogens=F)$resnames
+
 ```