diff --git a/collapse_scores.Rmd b/collapse_scores.Rmd index 3b4b08e..df737a5 100644 --- a/collapse_scores.Rmd +++ b/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} diff --git a/results/summary/collapse_scores.md b/results/summary/collapse_scores.md index a396257..36cd026 100644 --- a/results/summary/collapse_scores.md +++ b/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$final_variant_scores_dir,"/heatmap_SSM_delta-expression-by-target.pdf",sep=""))) ``` +And expression, hatchign out \>single-nt-accessible + +``` r +p1 <- ggplot(temp[measurement=="delta_expr" & chain != "link",],aes(position_IMGT,mutant))+geom_tile(aes(fill=value),color="black",lwd=0.1)+ + scale_fill_gradientn(colours=c("#A94E35","#F48365","#FFFFFF","#7378B9","#383C6C"),limits=c(-4,1),values=c(0/5,2/5,4/5,4.5/5,5/5),na.value="yellow")+ + #scale_x_continuous(expand=c(0,0),breaks=c(1,seq(5,235,by=5)))+ + labs(x="",y="")+theme_classic(base_size=9)+ + coord_equal()+theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.6,face="bold",size=10),axis.text.y=element_text(face="bold",size=10))+ + guides(y.sec=guide_axis_label_trans())+ + geom_text(aes(label=wildtype_indicator),size=2,color="gray10")+ + geom_text(aes(label=multimut_indicator),size=2.5,color="gray10") + +p1 +``` + + + +``` r +invisible(dev.print(pdf, paste(config$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 diff --git a/results/summary/collapse_scores_files/figure-gfm/heatmap_DMS_delta-expression-by-target_singlent-1.png b/results/summary/collapse_scores_files/figure-gfm/heatmap_DMS_delta-expression-by-target_singlent-1.png new file mode 100644 index 0000000..ae92b75 Binary files /dev/null and b/results/summary/collapse_scores_files/figure-gfm/heatmap_DMS_delta-expression-by-target_singlent-1.png differ diff --git a/results/summary/structural_mapping.md b/results/summary/structural_mapping.md index 093de8d..cd53e87 100644 --- a/results/summary/structural_mapping.md +++ b/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)" diff --git a/structural_mapping.Rmd b/structural_mapping.Rmd index b85ca87..c66dc90 100644 --- a/structural_mapping.Rmd +++ b/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 + ``` \ No newline at end of file