diff --git a/graphs/40_63_explore-synlet-comut/COAD_G12D_SRSF5-patch.svg b/graphs/40_63_explore-synlet-comut/COAD_G12D_SRSF5-patch.svg index 12073d6a..548d6410 100644 --- a/graphs/40_63_explore-synlet-comut/COAD_G12D_SRSF5-patch.svg +++ b/graphs/40_63_explore-synlet-comut/COAD_G12D_SRSF5-patch.svg @@ -28,25 +28,25 @@ - - - - + + + + - - - + + + - - + + - -G12D & APC - -APC + +G12D + +APC HECW1 @@ -55,9 +55,9 @@ 0.00 -0.05 -0.10 -0.15 +0.05 +0.10 +0.15 COAD estimated effect @@ -137,14 +137,14 @@ -0.2 0.0 0.2 -WT +neither APC HECW1 APC & HECW1 -dependency -score -of -FKBP1A +dependency +score +of +SRSF5 mutation diff --git a/graphs/40_63_explore-synlet-comut/COAD_G12D_SRSF5_coef-plot.svg b/graphs/40_63_explore-synlet-comut/COAD_G12D_SRSF5_coef-plot.svg index fbb2d48e..c009645d 100644 --- a/graphs/40_63_explore-synlet-comut/COAD_G12D_SRSF5_coef-plot.svg +++ b/graphs/40_63_explore-synlet-comut/COAD_G12D_SRSF5_coef-plot.svg @@ -17,25 +17,25 @@ - - - - + + + + - - - + + + - - + + - -G12D & APC - -APC + +G12D + +APC HECW1 @@ -44,9 +44,9 @@ 0.00 -0.05 -0.10 -0.15 +0.05 +0.10 +0.15 COAD estimated effect diff --git a/graphs/40_63_explore-synlet-comut/COAD_G12D_STARD9_coef-plot.svg b/graphs/40_63_explore-synlet-comut/COAD_G12D_STARD9_coef-plot.svg index b905235a..63b4b3be 100644 --- a/graphs/40_63_explore-synlet-comut/COAD_G12D_STARD9_coef-plot.svg +++ b/graphs/40_63_explore-synlet-comut/COAD_G12D_STARD9_coef-plot.svg @@ -33,13 +33,13 @@ - + G12D - + TRPM2 - + TP53 - + APC diff --git a/graphs/40_63_explore-synlet-comut/COAD_G12D_STARD9_line-plot.svg b/graphs/40_63_explore-synlet-comut/COAD_G12D_STARD9_line-plot.svg index 64866906..c5dcd8d9 100644 --- a/graphs/40_63_explore-synlet-comut/COAD_G12D_STARD9_line-plot.svg +++ b/graphs/40_63_explore-synlet-comut/COAD_G12D_STARD9_line-plot.svg @@ -31,24 +31,32 @@ - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/graphs/40_63_explore-synlet-comut/COAD_G12D_STARD9_patch.svg b/graphs/40_63_explore-synlet-comut/COAD_G12D_STARD9_patch.svg index b529a895..1390629e 100644 --- a/graphs/40_63_explore-synlet-comut/COAD_G12D_STARD9_patch.svg +++ b/graphs/40_63_explore-synlet-comut/COAD_G12D_STARD9_patch.svg @@ -44,13 +44,13 @@ - + G12D - + TRPM2 - + TP53 - + APC @@ -98,24 +98,32 @@ - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/graphs/40_63_explore-synlet-comut/PAAD_G12D_ABI1_coef-plot.svg b/graphs/40_63_explore-synlet-comut/PAAD_G12D_ABI1_coef-plot.svg index fa12d631..1acc781f 100644 --- a/graphs/40_63_explore-synlet-comut/PAAD_G12D_ABI1_coef-plot.svg +++ b/graphs/40_63_explore-synlet-comut/PAAD_G12D_ABI1_coef-plot.svg @@ -17,45 +17,38 @@ - - - - - - - - - - - - - - - - - - - - -G12D - -SYNE1 - -HMCN1 - -G12D & GPR98 - -ARID1A - -SMAD4 + + + + + + + + + + + + + + + + + +G12D + +ARID1A + +SMAD4 --0.1 -0.0 -0.1 +-0.05 +0.00 +0.05 +0.10 +0.15 PAAD estimated effect diff --git a/graphs/40_63_explore-synlet-comut/PAAD_G12D_ABI1_line-plot.svg b/graphs/40_63_explore-synlet-comut/PAAD_G12D_ABI1_line-plot.svg index 8b3f2a9e..1149da57 100644 --- a/graphs/40_63_explore-synlet-comut/PAAD_G12D_ABI1_line-plot.svg +++ b/graphs/40_63_explore-synlet-comut/PAAD_G12D_ABI1_line-plot.svg @@ -29,21 +29,29 @@ - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + diff --git a/graphs/40_63_explore-synlet-comut/PAAD_G12D_ABI1_patch.svg b/graphs/40_63_explore-synlet-comut/PAAD_G12D_ABI1_patch.svg index 563c9729..8c89ed82 100644 --- a/graphs/40_63_explore-synlet-comut/PAAD_G12D_ABI1_patch.svg +++ b/graphs/40_63_explore-synlet-comut/PAAD_G12D_ABI1_patch.svg @@ -28,45 +28,38 @@ - - - - - - - - - - - - - - - - - - - - -G12D - -SYNE1 - -HMCN1 - -G12D & GPR98 - -ARID1A - -SMAD4 + + + + + + + + + + + + + + + + + +G12D + +ARID1A + +SMAD4 --0.1 -0.0 -0.1 +-0.05 +0.00 +0.05 +0.10 +0.15 PAAD estimated effect @@ -103,21 +96,29 @@ - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + diff --git a/graphs/40_63_explore-synlet-comut/PAAD_G12D_EEF1E1_coef-plot.svg b/graphs/40_63_explore-synlet-comut/PAAD_G12D_EEF1E1_coef-plot.svg index 72a287ae..3e606ca8 100644 --- a/graphs/40_63_explore-synlet-comut/PAAD_G12D_EEF1E1_coef-plot.svg +++ b/graphs/40_63_explore-synlet-comut/PAAD_G12D_EEF1E1_coef-plot.svg @@ -17,37 +17,32 @@ - - - - - + + + + - - - - - - - - - - + + + + + + + + G12D - + SMAD4 --0.06 --0.04 --0.02 -0.00 -0.02 -0.04 +-0.04 +-0.02 +0.00 +0.02 PAAD estimated effect diff --git a/graphs/40_63_explore-synlet-comut/PAAD_G12D_EEF1E1_line-plot.svg b/graphs/40_63_explore-synlet-comut/PAAD_G12D_EEF1E1_line-plot.svg index 4e819a44..01b8cb2c 100644 --- a/graphs/40_63_explore-synlet-comut/PAAD_G12D_EEF1E1_line-plot.svg +++ b/graphs/40_63_explore-synlet-comut/PAAD_G12D_EEF1E1_line-plot.svg @@ -29,21 +29,29 @@ - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + diff --git a/graphs/40_63_explore-synlet-comut/PAAD_G12D_EEF1E1_patch.svg b/graphs/40_63_explore-synlet-comut/PAAD_G12D_EEF1E1_patch.svg index eab563ea..f251a004 100644 --- a/graphs/40_63_explore-synlet-comut/PAAD_G12D_EEF1E1_patch.svg +++ b/graphs/40_63_explore-synlet-comut/PAAD_G12D_EEF1E1_patch.svg @@ -28,37 +28,32 @@ - - - - - + + + + - - - - - - - - - - + + + + + + + + G12D - + SMAD4 --0.06 --0.04 --0.02 -0.00 -0.02 -0.04 +-0.04 +-0.02 +0.00 +0.02 PAAD estimated effect @@ -95,21 +90,29 @@ - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + diff --git a/graphs/40_63_explore-synlet-comut/PAAD_G12D_FKBP1A-patch.svg b/graphs/40_63_explore-synlet-comut/PAAD_G12D_FKBP1A-patch.svg index 1034f197..42b6f22a 100644 --- a/graphs/40_63_explore-synlet-comut/PAAD_G12D_FKBP1A-patch.svg +++ b/graphs/40_63_explore-synlet-comut/PAAD_G12D_FKBP1A-patch.svg @@ -28,35 +28,30 @@ - - - - - - - - - - + + + + + + + + - - - - -G12D - -G12D & GPR98 - -RNF43 + + + +G12D + +RNF43 --0.15 --0.10 --0.05 +-0.12 +-0.08 +-0.04 0.00 PAAD estimated diff --git a/graphs/40_63_explore-synlet-comut/PAAD_G12D_FKBP1A_coef-plot.svg b/graphs/40_63_explore-synlet-comut/PAAD_G12D_FKBP1A_coef-plot.svg index f7cb4b7c..763648fe 100644 --- a/graphs/40_63_explore-synlet-comut/PAAD_G12D_FKBP1A_coef-plot.svg +++ b/graphs/40_63_explore-synlet-comut/PAAD_G12D_FKBP1A_coef-plot.svg @@ -17,35 +17,30 @@ - - - - - - - - - - + + + + + + + + - - - - -G12D - -G12D & GPR98 - -RNF43 + + + +G12D + +RNF43 --0.15 --0.10 --0.05 +-0.12 +-0.08 +-0.04 0.00 PAAD estimated diff --git a/graphs/40_63_explore-synlet-comut/PAAD_G12D_MYBL2_coef-plot.svg b/graphs/40_63_explore-synlet-comut/PAAD_G12D_MYBL2_coef-plot.svg index 9c251753..24270083 100644 --- a/graphs/40_63_explore-synlet-comut/PAAD_G12D_MYBL2_coef-plot.svg +++ b/graphs/40_63_explore-synlet-comut/PAAD_G12D_MYBL2_coef-plot.svg @@ -17,41 +17,49 @@ - - - + + + + + - - - - - - - - - - + + + + + + + + + + + + + G12D - -HMCN1 - -LRP1B - -ARID1A - + +HMCN1 + +LRP1B + +ARID1A + SMAD4 --0.1 -0.0 -0.1 +-0.10 +-0.05 +0.00 +0.05 +0.10 +0.15 PAAD estimated effect diff --git a/graphs/40_63_explore-synlet-comut/PAAD_G12D_MYBL2_line-plot.svg b/graphs/40_63_explore-synlet-comut/PAAD_G12D_MYBL2_line-plot.svg index dded64a3..c878bb51 100644 --- a/graphs/40_63_explore-synlet-comut/PAAD_G12D_MYBL2_line-plot.svg +++ b/graphs/40_63_explore-synlet-comut/PAAD_G12D_MYBL2_line-plot.svg @@ -29,21 +29,29 @@ - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + diff --git a/graphs/40_63_explore-synlet-comut/PAAD_G12D_MYBL2_patch.svg b/graphs/40_63_explore-synlet-comut/PAAD_G12D_MYBL2_patch.svg index 43a283a2..cfe4d17d 100644 --- a/graphs/40_63_explore-synlet-comut/PAAD_G12D_MYBL2_patch.svg +++ b/graphs/40_63_explore-synlet-comut/PAAD_G12D_MYBL2_patch.svg @@ -28,41 +28,49 @@ - - - + + + + + - - - - - - - - - - + + + + + + + + + + + + + G12D - -HMCN1 - -LRP1B - -ARID1A - + +HMCN1 + +LRP1B + +ARID1A + SMAD4 --0.1 -0.0 -0.1 +-0.10 +-0.05 +0.00 +0.05 +0.10 +0.15 PAAD estimated effect @@ -99,21 +107,29 @@ - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + diff --git a/paper/figures/Fig_5.jpeg b/paper/figures/Fig_5.jpeg index 782f0ef9..657410c6 100644 Binary files a/paper/figures/Fig_5.jpeg and b/paper/figures/Fig_5.jpeg differ diff --git a/paper/figures/Fig_5.pdf b/paper/figures/Fig_5.pdf index d851274b..0ae4bf25 100644 Binary files a/paper/figures/Fig_5.pdf and b/paper/figures/Fig_5.pdf differ diff --git a/paper/figures/Fig_5.svg b/paper/figures/Fig_5.svg index 08212794..c13e38b5 100644 --- a/paper/figures/Fig_5.svg +++ b/paper/figures/Fig_5.svg @@ -1,5 +1,5 @@ - + - + - - + + - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - -G12D - -TRPM2 - -TP53 - -APC + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +G12D + +TRPM2 + +TP53 + +APC - - + + -0.00 -0.05 -0.10 -estimate -COAD -estimated -effect -of -mutation -on -dependency -on -STARD9 -a +-0.05 +0.00 +0.05 +0.10 +0.15 +estimated +effect +Effect +of +mutation +on +STARD9 +dep. +COAD +a - - + + - + - - + + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - --0.2 --0.1 -0.0 -0.1 -TP53 -G12D -dependency -score -of -STARD9 - - - - + + + - +-0.2 +-0.1 +0.0 +0.1 +TP53 +G12D +dependency +score +of +STARD9 - - + + - - + + - -reduced -comutation - -G12D - -TP53 - - + + - - + + - - + + + + + + + + + + + + + + + + + +G12D + +SMAD4 - - + + +-0.04 +-0.02 +0.00 +0.02 +estimated +effect +Effect +of +mutation +on +EEF1E1 +dep. +PAAD +b - - + + - - - - - - - - - - - - - - - - - - - - - - - -G12D - -SMAD4 + + - - + + --0.06 --0.04 --0.02 -0.00 -0.02 -0.04 -estimate -PAAD -estimated -effect -of -mutation -on -dependency -on -EEF1E1 -b - - + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + +-0.8 +-0.6 +-0.4 +-0.2 +SMAD4 +G12D +dependency +score +of +EEF1E1 - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - --0.8 --0.6 --0.4 --0.2 -SMAD4 -G12D -dependency -score -of -EEF1E1 - - - - - - - - - - - - - - - - - -reduced -comutation - -G12D - -SMAD4 - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +G12D + +ARID1A + +SMAD4 + + + + + +0.0 +0.1 +estimated +effect +Effect +of +mutation +on +ABI1 +dep. +PAAD +c + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-0.4 +-0.2 +0.0 +SMAD4 +G12D +dependency +score +of +ABI1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +G12D + +HMCN1 + +LRP1B + +ARID1A + +SMAD4 + + + + + +-0.10 +-0.05 +0.00 +0.05 +0.10 +0.15 +estimated +effect +Effect +of +mutation +on +MYBL2 +dep. +PAAD +d + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-1.00 +-0.75 +-0.50 +-0.25 +SMAD4 +G12D +dependency +score +of +MYBL2 + + + + + + + + + + + + + + + + + + + + + + + + + + + +reduced +comutation + +G12D + +TP53 + + + + + + + + + + + + + + + + + + + + + + +reduced +comutation + +G12D + +SMAD4 + + + diff --git a/paper/figures/Fig_6.jpeg b/paper/figures/Fig_6.jpeg deleted file mode 100644 index 05b94cf0..00000000 Binary files a/paper/figures/Fig_6.jpeg and /dev/null differ diff --git a/paper/figures/Fig_6.pdf b/paper/figures/Fig_6.pdf deleted file mode 100644 index bf839a32..00000000 Binary files a/paper/figures/Fig_6.pdf and /dev/null differ diff --git a/paper/figures/Fig_6.svg b/paper/figures/Fig_6.svg deleted file mode 100644 index abc0ec28..00000000 --- a/paper/figures/Fig_6.svg +++ /dev/null @@ -1,575 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -G12D & APC - -APC - -HECW1 - - - - - -0.00 -0.05 -0.10 -0.15 -estimate -COAD -estimated -effect -of -mutation -on -dependency -on -SRSF5 -a - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - --0.6 --0.4 --0.2 -0.0 -0.2 -neither -APC -HECW1 -APC & -HECW1 -dependency -score -of -SRSF5 - - - - - - - -G12D -APC/HECW1 -neither - - - - - - - - - - - - - - - - - - -reduced -comutation -increased -comutation - -G12D - -HECW1 - -APC - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -G12R - -DNAH5 - - - - - --0.06 --0.04 --0.02 -0.00 -estimate -PAAD -estimated -effect -of -mutation -on -dependency -on -KIAA1257 -b - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - --0.2 --0.1 -0.0 -0.1 -neither -DNAH5 -G12R -DNAH5 & -G12R -dependency -score -of -KIAA1257 - - - - - - - - - -neither -DNAH5 -G12R -DNAH5 & G12R - - - - - - - - - - - - - - - - - -reduced -comutation - -G12R - -DNAH5 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -G12D - -G12D & GPR98 - -RNF43 - - - - - --0.20 --0.15 --0.10 --0.05 -0.00 -estimate -PAAD -estimated -effect -of -mutation -on -dependency -on -FKBP1A -c - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - --0.4 --0.2 -0.0 -neither -GPR98 -RNF43 -GPR98 & -RNF43 -dependency -score -of -FKBP1A - - - - - - - -neither -GPR98/RNF43 -G12D - - - - - - - - - - - - - - - - - - -increased -comutation -increased -comutation - -G12D - -RNF43 - -GPR98 - - - - - - diff --git a/paper/figures/Supp_Fig_8.jpeg b/paper/figures/Supp_Fig_8.jpeg deleted file mode 100644 index 6fc394cc..00000000 Binary files a/paper/figures/Supp_Fig_8.jpeg and /dev/null differ diff --git a/paper/figures/Supp_Fig_8.pdf b/paper/figures/Supp_Fig_8.pdf deleted file mode 100644 index aff29e6a..00000000 Binary files a/paper/figures/Supp_Fig_8.pdf and /dev/null differ diff --git a/paper/figures/Supp_Fig_8.svg b/paper/figures/Supp_Fig_8.svg deleted file mode 100644 index ccd0cc91..00000000 --- a/paper/figures/Supp_Fig_8.svg +++ /dev/null @@ -1,277 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -G12D - -SYNE1 - -HMCN1 - -G12D & GPR98 - -ARID1A - -SMAD4 - - - - - --0.1 -0.0 -0.1 -estimate -PAAD -estimated -effect -of -mutation -on -dependency -on -ABI1 -a - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - --0.4 --0.2 -0.0 -SMAD4 -G12D -dependency -score -of -ABI1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -G12D - -HMCN1 - -LRP1B - -ARID1A - -SMAD4 - - - - - --0.1 -0.0 -0.1 -estimate -PAAD -estimated -effect -of -mutation -on -dependency -on -MYBL2 -b - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - --1.00 --0.75 --0.50 --0.25 -SMAD4 -G12D -dependency -score -of -MYBL2 - diff --git a/paper/figures/all_images/figure_048.jpeg b/paper/figures/all_images/figure_048.jpeg new file mode 100644 index 00000000..657410c6 Binary files /dev/null and b/paper/figures/all_images/figure_048.jpeg differ diff --git a/paper/figures/all_images/figure_048.svg b/paper/figures/all_images/figure_048.svg new file mode 100644 index 00000000..c13e38b5 --- /dev/null +++ b/paper/figures/all_images/figure_048.svg @@ -0,0 +1,631 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +G12D + +TRPM2 + +TP53 + +APC + + + + + +-0.05 +0.00 +0.05 +0.10 +0.15 +estimated +effect +Effect +of +mutation +on +STARD9 +dep. +COAD +a + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-0.2 +-0.1 +0.0 +0.1 +TP53 +G12D +dependency +score +of +STARD9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +G12D + +SMAD4 + + + + + +-0.04 +-0.02 +0.00 +0.02 +estimated +effect +Effect +of +mutation +on +EEF1E1 +dep. +PAAD +b + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-0.8 +-0.6 +-0.4 +-0.2 +SMAD4 +G12D +dependency +score +of +EEF1E1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +G12D + +ARID1A + +SMAD4 + + + + + +0.0 +0.1 +estimated +effect +Effect +of +mutation +on +ABI1 +dep. +PAAD +c + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-0.4 +-0.2 +0.0 +SMAD4 +G12D +dependency +score +of +ABI1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +G12D + +HMCN1 + +LRP1B + +ARID1A + +SMAD4 + + + + + +-0.10 +-0.05 +0.00 +0.05 +0.10 +0.15 +estimated +effect +Effect +of +mutation +on +MYBL2 +dep. +PAAD +d + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-1.00 +-0.75 +-0.50 +-0.25 +SMAD4 +G12D +dependency +score +of +MYBL2 + + + + + + + + + + + + + + + + + + + + + + + + + + + +reduced +comutation + +G12D + +TP53 + + + + + + + + + + + + + + + + + + + + + + +reduced +comutation + +G12D + +SMAD4 + + + + + + diff --git a/paper/figures/figure_conversion.json b/paper/figures/figure_conversion.json index fee6f172..0c29e421 100644 --- a/paper/figures/figure_conversion.json +++ b/paper/figures/figure_conversion.json @@ -21,12 +21,7 @@ }, { "figure_num": 5, - "make_num": 45, - "supp": false - }, - { - "figure_num": 6, - "make_num": 46, + "make_num": 48, "supp": false }, @@ -66,11 +61,6 @@ "figure_num": 7, "make_num": 34, "supp": true - }, - { - "figure_num": 8, - "make_num": 47, - "supp": true } ] \ No newline at end of file diff --git a/paper/figures/make_figure_scripts/make-figure_048.R b/paper/figures/make_figure_scripts/make-figure_048.R new file mode 100644 index 00000000..19fe62a5 --- /dev/null +++ b/paper/figures/make_figure_scripts/make-figure_048.R @@ -0,0 +1,186 @@ +# Figure 048. #> The group of results from the analysis for explaining +# allele-specific genetic dependency by comutation. + +FIGNUM <- 48 + +#> SET THE FIGURE DIMENSIONS +FIG_DIMENSIONS <- get_figure_dimensions(2, "short") +FIG_DIMENSIONS$height <- 100 + +theme_fig48 <- function(tag_margin = margin(-1, -1, -1, -1, "mm")) { + theme_comutation() %+replace% + theme( + legend.title = element_blank(), + plot.tag = element_text(size = 7, + face = "bold", + margin = tag_margin) + ) +} + + +theme_fig48 <- function(tag_margin = margin(-1, -1, -1, -1, "mm")) { + theme_comutation() %+replace% + theme( + legend.title = element_blank(), + plot.tag = element_text(size = 7, + face = "bold", + margin = tag_margin) + ) +} + + +theme_coefplot_fig48 <- function(tag_margin = margin(-1, -1, -2, -1, "mm")) { + theme_minimal_comutation() %+replace% + theme( + plot.title = element_markdown(size = 7, + face = "bold", + family = "Arial", + hjust = 0, + halign = 0), + plot.subtitle = element_markdown(size = 6, + face = "bold", + family = "Arial", + hjust = 0, + halign = 0), + plot.tag = element_text(size = 7, + face = "bold", + margin = tag_margin), + legend.position = "none", + axis.text.y = element_blank(), + axis.title.y = element_blank(), + axis.title.x = element_markdown() + ) +} + + +theme_boxplot_fig48 <- function(tag_margin = margin(-1, -1, -1, -1, "mm")) { + theme_fig48(tag_margin = tag_margin) %+replace% + theme( + legend.position = "none", + axis.title.y = element_markdown(angle = 90, hjust = 0.5, vjust = 0.5), + axis.title.x = element_blank() + ) +} + + +theme_fig48_void <- function(tag_margin = margin(-1, -1, -1, -1, "mm")) { + theme_graph_comutation() %+replace% + theme( + plot.tag = element_text(size = 7, + face = "bold", + margin = tag_margin), + plot.margin = margin(1, -1, -1, -1, "mm") + ) +} + +get_coef_plot_title <- function(cancer, gene) { + glue("{cancer}
Effect of mutation on *{gene}* dep.") +} + +get_coef_plot_subtitle <- function(gene) { + glue("Effect of mutation on *{gene}* dep.") +} + + +#### ---- A. TP53 explaining STARD9 ---- #### +# TP53 explaining dep. of G12D on STARD9 in COAD. +# original script: "src/40_63_explore-synlet-comut.R" + +panel_A_1 <- read_fig_proto("COAD_G12D_STARD9_coef-plot") + + scale_x_continuous(expand = expansion(mult = c(0.17, 0.15))) + + theme_coefplot_fig48() + + labs(tag = "a", + x = "estimated effect", + title = "COAD", + subtitle = get_coef_plot_subtitle("STARD9")) +panel_A_2 <- read_fig_proto("COAD_G12D_STARD9_line-plot") + + theme_boxplot_fig48() +panel_A_3 <- read_fig_proto("COAD_G12D_TP53_comut-graph-plot.rds") + + scale_x_continuous(expand = expansion(mult = c(0.50, 0.50))) + + theme_fig48_void() + +panel_A <- (panel_A_1 / panel_A_2 ) + + plot_layout(height = c(3, 7)) + + + +#### ---- B. SMAD4 explaining EEF1E1 ---- #### +# SMAD4 explaining dep. of G12D on EEF1E1 in PAAD. +# original script: "src/40_63_explore-synlet-comut.R" + +panel_B_1 <- read_fig_proto("PAAD_G12D_EEF1E1_coef-plot") + + scale_x_continuous(expand = expansion(mult = c(0.17, 0.15))) + + theme_coefplot_fig48() + + labs(tag = "b", + x = "estimated effect", + title = "PAAD", + subtitle = get_coef_plot_subtitle("EEF1E1")) +panel_B_2 <- read_fig_proto("PAAD_G12D_EEF1E1_line-plot") + + theme_boxplot_fig48() +panel_BCD_3 <- read_fig_proto("PAAD_G12D_SMAD4_comut-graph-plot.rds") + + scale_x_continuous(expand = expansion(mult = c(0.50, 0.50))) + + theme_fig48_void() + +panel_B <- (panel_B_1 / panel_B_2) + + plot_layout(height = c(3, 7)) + + +#### ---- C. SMAD4 explaining ABI1 ---- #### +# SMAD4 explaining dep. of G12D on ABI1 in PAAD. +# original script: "src/40_63_explore-synlet-comut.R" + +panel_C_1 <- read_fig_proto("PAAD_G12D_ABI1_coef-plot") + + scale_x_continuous(expand = expansion(mult = c(0.17, 0.15))) + + theme_coefplot_fig48() + + labs(tag = "c", + x = "estimated effect", + title = "PAAD", + subtitle = get_coef_plot_subtitle("ABI1")) +panel_C_2 <- read_fig_proto("PAAD_G12D_ABI1_line-plot") + + theme_boxplot_fig48() + + +panel_C <- (panel_C_1 / panel_C_2) + + plot_layout(height = c(3, 7)) + + + +#### ---- D. SMAD4 explaining MYBL2 ---- #### +# SMAD4 explaining dep. of G12D on MYBL2 in PAAD. +# original script: "src/40_63_explore-synlet-comut.R" + +panel_D_1 <- read_fig_proto("PAAD_G12D_MYBL2_coef-plot") + + scale_x_continuous(expand = expansion(mult = c(0.17, 0.15))) + + theme_coefplot_fig48() + + labs(tag = "d", + x = "estimated effect", + title = "PAAD", + subtitle = get_coef_plot_subtitle("MYBL2")) +panel_D_2 <- read_fig_proto("PAAD_G12D_MYBL2_line-plot") + + theme_boxplot_fig48() + +panel_D <- (panel_D_1 / panel_D_2) + + plot_layout(height = c(3, 7)) + + + +#### ---- Figure assembly ---- #### + +{ + # COMPLETE FIGURE + full_figure <- ( + (( + panel_A | panel_B | panel_C | panel_D + ) + plot_layout(widths = c(1, 1, 1, 1))) / + (( + panel_A_3 | panel_B_3 + ) + plot_layout(widths = c(1, 3))) + ) + + plot_layout(heights = c(10, 2)) + + save_figure( + full_figure, + figure_num = FIGNUM, + dim = FIG_DIMENSIONS + ) +} diff --git a/src/40_60_synlet-explained-by-comuts.R b/src/40_60_synlet-explained-by-comuts.R index 5472082e..5fc4e694 100644 --- a/src/40_60_synlet-explained-by-comuts.R +++ b/src/40_60_synlet-explained-by-comuts.R @@ -467,3 +467,23 @@ cache("synlet_comut_model_res", plt = map2(name, fit, synlet_with_comutations_plots)) return(synlet_comut_model_res) }) + +synlet_comut_model_res %>% + count(cancer, allele, num_coefs, name = "num_genes") %>% + arrange(cancer, allele, num_coefs) %>% + knitr::kable() +#> |cancer |allele | num_coefs| num_genes| +#> |:------|:------|---------:|---------:| +#> |COAD |G12D | 37| 3| +#> |COAD |G12D | 44| 27| +#> |COAD |G12D | 45| 8| +#> |COAD |G12V | 28| 7| +#> |COAD |G12V | 29| 1| +#> |COAD |G13D | 15| 12| +#> |COAD |G13D | 16| 1| +#> |PAAD |G12D | 12| 1| +#> |PAAD |G12D | 14| 2| +#> |PAAD |G12D | 15| 73| +#> |PAAD |G12R | 13| 1| +#> |PAAD |G12R | 14| 63| +#> |PAAD |G12V | 8| 57| \ No newline at end of file diff --git a/src/40_63_explore-synlet-comut.R b/src/40_63_explore-synlet-comut.R index 523bf2ff..b54209f4 100644 --- a/src/40_63_explore-synlet-comut.R +++ b/src/40_63_explore-synlet-comut.R @@ -10,7 +10,6 @@ pastel_blue <- "#4096B3" set.seed(0) - ################################################################################ ## REMOVE FOR O2 ## @@ -43,14 +42,14 @@ set.seed(0) # load("cache/synlet_comut_model_res.RData") -# synlet_comut_model_res %<>% -# filter( -# (cancer == "COAD" & allele == "G12D" & hugo_symbol == "STARD9") | -# (cancer == "PAAD" & allele == "G12D" & hugo_symbol == "EEF1E1") | -# (cancer == "COAD" & allele == "G12D" & hugo_symbol == "SRSF5") | -# (cancer == "PAAD" & allele == "G12R" & hugo_symbol == "KIAA1257") | -# (cancer == "PAAD" & allele == "G12D" & hugo_symbol == "FKBP1A") -# ) +# # synlet_comut_model_res %<>% +# # filter( +# # (cancer == "COAD" & allele == "G12D" & hugo_symbol == "STARD9") | +# # (cancer == "PAAD" & allele == "G12D" & hugo_symbol == "EEF1E1") | +# # (cancer == "COAD" & allele == "G12D" & hugo_symbol == "SRSF5") | +# # (cancer == "PAAD" & allele == "G12R" & hugo_symbol == "KIAA1257") | +# # (cancer == "PAAD" & allele == "G12D" & hugo_symbol == "FKBP1A") +# # ) # load("cache/genetic_interaction_gr.RData") @@ -87,7 +86,7 @@ make_mask_coef_plot <- function(cancer, allele, hugo_symbol, fit, ...) { geom_segment(aes(yend = term, color = estimate), xend = 0, size = 1) + geom_label(aes(label = term, fill = estimate), family = "Arial", size = 2.2, - label.padding = unit(0.8, "mm"), + label.padding = unit(0.4, "mm"), label.r = unit(0.4, "mm"), color = "black", label.size = 0) + scale_color_gradient2(high = pastel_red, @@ -144,7 +143,8 @@ make_mask_line_plot <- function(cancer, allele, hugo_symbol, fit, other_gene, } p <- p + - ggbeeswarm::geom_quasirandom(size = 3, alpha = 0.7, groupOnX = TRUE) + + geom_boxplot(fill = NA, outlier.shape = NA) + + ggbeeswarm::geom_quasirandom(size = 1, alpha = 0.9, groupOnX = TRUE) + scale_color_manual(values = mask_pal, drop = TRUE) + scale_y_continuous(expand = expansion(mult = c(0.05, 0.05))) + theme_bw(base_size = 7, base_family = "Arial") + @@ -199,7 +199,7 @@ synlet_comut_model_res %>% -################################################################################ + ################################################################################ ################################################################################ ################################################################################