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create_krasddpcams.R
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rm(list=ls())
###beginning
library(ggpubr)
library(GGally)
#library(bio3d)
library(ggplot2)
library(plotly)
library(ComplexHeatmap)
library(circlize)
library(seqinr)
library(caTools)
library(pROC)
library(readr)
library(knitr)
library(PRROC)
library(rgl)
library(ggVennDiagram)
library(ggstatsplot)
library(plot3D)
library("devtools")
library(roxygen2)
#library(data.table)
library(ROCR)
library(openxlsx)
library(ggrepel)
#library(Cairo)
######
setwd("/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/")
#
library("devtools")
library(roxygen2)
#create("krasddpcams")
setwd("./krasddpcams")
document()
setwd("..")
library("krasddpcams")
######
#basic setting
######
options(ggrepel.max.overlaps = Inf)
colour_scheme<- list(
"blue"="#1B38A6",#rgb(27, 56, 166)
"red"="#F4270C",#rgb(244, 39, 12)
"orange"="#F4AD0C",#rgb(244, 173, 12)
"green"="#09B636",#rgb(9, 182, 54)
"yellow"="#F1DD10",#rgb(241, 221, 16)
"purple"="#6D17A0",#rgb(109, 23, 160)
"pink"="#FFB0A5",#rgb(255, 176, 165)
"light orange"="#FFE4A5",#rgb(255, 228, 165)
"light blue"="#9DACE3",#rgb(157, 172, 227)
"light green"="#97E9AD",#rgb(151, 233, 173)
"light red"="#FF6A56",#rgb(255, 106, 86)
"dark red"="#A31300",#rgb(163, 19, 0)
"dark blue"="#0C226F",#rgb(12, 34, 111)
"dark green"="#007A20"#rgb(0, 122, 32)
)
aa_list <- as.list(unlist(strsplit("GAVLMIFYWKRHDESTCNQP", "")))
######
#KRAS information
######
wt_aa<-"TEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKCVIM"
###beta strands
rects<-data.frame(xstart=c(2,37,49,77,111,141),
xend=c(10,46,58,83,116,143),
col=c("b1","b2","b3","b4","b5","b6"))
###alpha helix 1
rects_alpha<-data.frame(xstart=c(16),
xend=c(25
),
col=c("a1"))
###all alpha helix
rects_alpha_all<-data.frame(xstart=c(16,62,87,127, 152),
xend=c(25,74,104, 137,166 ),
col=c("a1","a2","a3","a4","a5"))
##
all_distance_anno<-fread("./DATA/all_distance_anno.csv")
all_long_distance<-fread("./DATA/all_long_distance.csv")
all_long_distance_GXPMG<-fread("./DATA/all_long_distance_GXPMG.csv")
final_distance_dc_anno_for_anno_mt_5<-fread("./DATA/final_distance_dc_anno_for_anno_mt_5.csv")
anno_final3<-fread("./DATA/anno_final3.csv")
######
#loading data
######
stability_nor_df <- Normalize_growthrate_fitness(block1_dimsum_df = "./DATA/CW_RAS_abundance_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "./DATA/CW_RAS_abundance_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "./DATA/CW_RAS_abundance_3_fitness_replicates_fullseq.RData")
RAF_nor_df <- Normalize_growthrate_fitness(block1_dimsum_df = "./DATA/CW_RAS_binding_RAF_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "./DATA/CW_RAS_binding_RAF_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "./DATA/CW_RAS_binding_RAF_3_fitness_replicates_fullseq.RData")
PI3_nor_df <- Normalize_growthrate_fitness(block1_dimsum_df = "./DATA/CW_RAS_binding_PI3_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "./DATA/CW_RAS_binding_PI3_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "./DATA/CW_RAS_binding_PI3_3_fitness_replicates_fullseq.RData")
RAL_nor_df <- Normalize_growthrate_fitness(block1_dimsum_df = "./DATA/CW_RAS_binding_RAL_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "./DATA/CW_RAS_binding_RAL_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "./DATA/CW_RAS_binding_RAL_3_fitness_replicates_fullseq.RData")
SOS_nor_df <- Normalize_growthrate_fitness(block1_dimsum_df = "./DATA/CW_RAS_binding_SOS_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "./DATA/CW_RAS_binding_SOS_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "./DATA/CW_RAS_binding_SOS_3_fitness_replicates_fullseq.RData")
K27_nor_df <- Normalize_growthrate_fitness(block1_dimsum_df = "./DATA/CW_RAS_binding_K27_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "./DATA/CW_RAS_binding_K27_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "./DATA/CW_RAS_binding_K27_3_fitness_replicates_fullseq.RData")
K55_nor_df <- Normalize_growthrate_fitness(block1_dimsum_df = "./DATA/CW_RAS_binding_K55_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "./DATA/CW_RAS_binding_K55_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "./DATA/CW_RAS_binding_K55_3_fitness_replicates_fullseq.RData")
stab <- stability_nor_df
RAF <- RAF_nor_df
K27 <- K27_nor_df
PI3 <- PI3_nor_df
RAL <- RAL_nor_df
SOS <- SOS_nor_df
K55 <- K55_nor_df
all_data <- Merge_dimsum_df(stab,RAF,K27,PI3,RAL,SOS,K55)
all_data_pos<-Pos_id(all_data,wt_aa)
fullRAF_nor_df <- Normalize_growthrate_fitness_block1(block1_dimsum_df = "/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/0628_merge_data/CW_RAS_binding_FULLRAF_1_fitness_replicates.RData")
fullRAF_nor_df_pos<-Pos_id(fullRAF_nor_df,wt_aa)
GAP_nor_df <- Normalize_growthrate_fitness_block1(block1_dimsum_df = "/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/GAP_PCA_data/CW_RAS_binding_RAFGAP_1_fitness_replicates_fullseq.RData")
GAP_nor_df_pos<-Pos_id(GAP_nor_df,wt_aa)
RAF_nor_df_pos<-Pos_id(RAF_nor_df,wt_aa)
######
#figure 1
######
#1e
Plot_heatmap_fitness(all_data_pos,"stab",anno_final3)+
theme(axis.text.y = element_text(family="Courier New",angle=90,size=5, vjust =.5,hjust =.5,margin=margin(0,-0.5,0,0,"mm")))
#1f
Plot_heatmap_fitness(all_data_pos,"RAF",anno_final3)+
theme(axis.text.y = element_text(family="Courier New",angle=90,size=5, vjust =.5,hjust =.5,margin=margin(0,-0.5,0,0,"mm")))
#1g
Plot_heatmap_ddG(input="./DATA/weights_Folding.txt",
assay_name = "folding")
#1h
Plot_heatmap_ddG(input="./DATA/weights_Binding_RAF.txt",
assay_name = "RAF1")
#1j
Scatterplot_fitness_bs(input = all_data_pos,
assay_sele="RAF",
anno = anno_final3)
#1k
Plot_RAF_invitro_cor(input="./DATA/weights_Binding_RAF.txt",
assay_name = "RAF1")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figure1k_RAF1_invitro_ddG_cor.pdf", device = cairo_pdf,height = 50,width=50,units = "mm")
#1h
Weighted_mean_ddG_structure(ddG="./DATA/weights_Folding.txt",
input_PDB = "./DATA/pdb6vjj.ent",
chain_KRAS = "A",
output_PDB_file="./results/figure1H_folding_ddG_pdb6vjj.pdb")
#to make figure 1h using chimeraX
######
#figure 2
######
#2A
Plot_scatter_ddGb_ddGf(ddG1="./DATA/weights_Folding.txt",
assay1="folding",
ddG2="./DATA/weights_Binding_RAF.txt",
assay2="RAF1",
anno=anno_final3)
#2B
weighted_mean_abs_ddG_fold<-Get_weighted_mean_abs_ddG(ddG="./DATA/weights_Folding.txt",
assay_sele = "folding")
weighted_mean_abs_ddG_RAF<-Get_weighted_mean_abs_ddG(ddG="./DATA/weights_Binding_RAF.txt",
assay_sele = "RAF")
Plot_ROCAUC_ddG_fitness_binding_interface(fitness_all=all_data_pos,
weighted_meab_abs_ddGf=weighted_mean_abs_ddG_fold,
weighted_meab_abs_ddGb=weighted_mean_abs_ddG_RAF,
anno_input=anno_final3,
bind="RAF",
bind_ligand = "scHAmin_ligand_RAF")+ggtitle("RAF1")
#2C
Weighted_mean_ddG_structure_fromweighteddata(weighted_mean_ddG=weighted_mean_abs_ddG_RAF,
input_PDB = "./DATA/pdb6vjj.ent",
chain_KRAS = "A",
output_PDB_file="./DATA/figure2C_RAF_binding_ab_ddG_6vjj.pdb")
#to make figure 2C using chimeraX, key command: color bfactor /A range -2,2
#2D
Plot_binding_interface_mutation_heatmap("./DATA/weights_Binding_RAF.txt",
assay_sele = "RAF1")
######
#figure 3
######
#3a
Plot_allosteric_mutations(ddG="./DATA/weights_Binding_RAF.txt",
anno=anno_final3,
assay_sele="RAF",
rect_input=rects,
rect_alpha=rects_alpha)
#3b
RAF_list<-Plot_major_allosteric_site(ddG="./DATA/weights_Binding_RAF.txt",
anno=anno_final3,
assay_name="RAF",
allosteric_list = RAF_list,
rect_input=rects)
RAF_list[["p"]]
#3c
#pdb 6vjj, chimeraX,
#paste0(RAF_list[["Binding interface site"]],collapse=",")
#paste0(RAF_list[["Allosteric GTP pocket site"]],collapse=",")
#paste0(RAF_list[["Major allosteric site"]],collapse=",")
#3d
Maximum_ddG_structure(ddG="./DATA/weights_Binding_RAF.txt",
input_PDB = "./DATA/pdb6vjj.ent",
chain_KRAS = "A",
output_PDB_file="./DATA/figure3D_max_RAF_binding_ddG_6vjj.pdb")
#to make figure3d using chimeraX, key: color bfactor /A range -2,2
#3e
Plot_ddG_betasheet(ddG="./DATA/weights_Binding_RAF.txt",
weighted_mean_ddG=weighted_mean_abs_ddG_RAF,
anno=anno_final3,
assay_sele="RAF",
rect_input=rects)
#3f
#6vjj and 6oim, using chimeraX, key: merge #1/A to #2/B
#3g
Maximum_ddG_structure(ddG="./DATA/weights_Binding_RAF.txt",
input_PDB = "./DATA/pdb6oim.ent",
chain_KRAS = "A",
output_PDB_file="./DATA/figure3D_max_RAF_binding_ddG_6oim.pdb")
#to make figure3g using chimeraX, key:color bfactor sel range -2,2
######
#figure 4
######
#4a
Plot_figure4A_point_all_ddG_alphabeta(ddG1="./DATA/weights_Folding.txt",
assay1="folding",
ddG2="./DATA/weights_Binding_RAF.txt",
assay2="RAF1",
ddG3="./DATA/weights_Binding_PI3.txt",
assay3="PIK3CG",
ddG4="./DATA/weights_Binding_RAL.txt",
assay4="RALGDS",
ddG5="./DATA/weights_Binding_SOS.txt",
assay5="SOS1",
ddG6="./DATA/weights_Binding_K27.txt",
assay6="DARPin K27",
ddG7="./DATA/weights_Binding_K55.txt",
assay7="DARPin K55",
anno=final_distance_dc_anno_for_anno_mt_5,
rect_input=rects,
rect_alpha = rects_alpha)
#4b
Plot_RAL_invitro_cor_ITC(ddG="./DATA/weights_Binding_RAL.txt",
assay_sele = "RAL")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figure4b_RALGDS_ITC_invitro_ddG_cor.pdf", device = cairo_pdf,height = 40,width=40,units = "mm")
#4c
Plot_RAL_invitro_cor_GDI(ddG="./DATA/weights_Binding_RAL.txt",
assay_sele = "RAL")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figure4c_RALGDS_GDI_invitro_ddG_cor.pdf", device = cairo_pdf,height = 45,width=45,units = "mm")
######
#figure 5
######
#5a
figure5A<-Get_common_interface(anno_input=anno_final3)
figure5A[["p"]]
#5b
#top
#to make figure5b, use chimeraX color binding interface residues
#binding interface residues of 5 binding partners
# paste0(figure5A[["matrix"]][assay=="K55"&binding=="yes",Pos],collapse=",")
# paste0(figure5A[["matrix"]][assay=="K55"&binding=="common",Pos],collapse=",")
# paste0(figure5A[["matrix"]][assay=="K27"&binding=="yes",Pos],collapse=",")
# paste0(figure5A[["matrix"]][assay=="K27"&binding=="common",Pos],collapse=",")
# paste0(figure5A[["matrix"]][assay=="RAL"&binding=="yes",Pos]+200,collapse=",")
# paste0(figure5A[["matrix"]][assay=="RAL"&binding=="common",Pos]+200,collapse=",")
# paste0(figure5A[["matrix"]][assay=="SOS"&binding=="yes",Pos],collapse=",")
# paste0(figure5A[["matrix"]][assay=="SOS"&binding=="common",Pos],collapse=",")
# paste0(figure5A[["matrix"]][assay=="PI3"&binding=="yes",Pos],collapse=",")
# paste0(figure5A[["matrix"]][assay=="PI3"&binding=="common",Pos],collapse=",")
# paste0(figure5A[["matrix"]][assay=="RAF"&binding=="yes",Pos],collapse=",")
# paste0(figure5A[["matrix"]][assay=="RAF"&binding=="common",Pos],collapse=",")
#bottom
#RAF
Weighted_mean_ddG_structure_fromweighteddata(weighted_mean_ddG=weighted_mean_abs_ddG_RAF,
input_PDB = "./DATA/pdb6vjj.ent",
chain_KRAS = "A",
output_PDB_file="./DATA/figure5C_RAF_binding_ab_ddG_6vjj.pdb")
#PI3
weighted_mean_abs_ddG_PI3<-Get_weighted_mean_abs_ddG(ddG="./DATA/weights_Binding_PI3.txt",
assay_sele = "PI3")
Weighted_mean_ddG_structure_fromweighteddata(weighted_mean_ddG=weighted_mean_abs_ddG_PI3,
input_PDB = "./DATA/pdb1he8.ent",
chain_KRAS = "B",
output_PDB_file="./DATA/figure5C_PI3_binding_ab_ddG_1he8.pdb")
#RAL
weighted_mean_abs_ddG_RAL<-Get_weighted_mean_abs_ddG(ddG="./DATA/weights_Binding_RAL.txt",
assay_sele = "RAL")
Weighted_mean_ddG_structure_fromweighteddata(weighted_mean_ddG=weighted_mean_abs_ddG_RAL,
input_PDB = "./DATA/pdb1lfd.ent",
chain_KRAS = "B",
Pos_correction=200,
output_PDB_file="./DATA/figure5C_RAL_binding_ab_ddG_1lfd.pdb")
#SOS
weighted_mean_abs_ddG_SOS<-Get_weighted_mean_abs_ddG(ddG="./DATA/weights_Binding_SOS.txt",
assay_sele = "SOS")
Weighted_mean_ddG_structure_fromweighteddata(weighted_mean_ddG=weighted_mean_abs_ddG_SOS,
input_PDB = "./DATA/1nvw.pdb",
chain_KRAS = "R",
output_PDB_file="./DATA/figure5C_SOS_binding_ab_ddG_1nvw_R.pdb")
Weighted_mean_ddG_structure_fromweighteddata(weighted_mean_ddG=weighted_mean_abs_ddG_SOS,
input_PDB = "./DATA/figure5C_SOS_binding_ab_ddG_1nvw_R.pdb",
chain_KRAS = "Q",
output_PDB_file="./DATA/figure5C_SOS_binding_ab_ddG_1nvv_RQ.pdb")
#K27
weighted_mean_abs_ddG_K27<-Get_weighted_mean_abs_ddG(ddG="./DATA/weights_Binding_K27.txt",
assay_sele = "K27")
Weighted_mean_ddG_structure_fromweighteddata(weighted_mean_ddG=weighted_mean_abs_ddG_K27,
input_PDB = "./DATA/pdb5o2s.ent",
chain_KRAS = "A",
output_PDB_file="./DATA/figure5C_K27_binding_ab_ddG_5o2s.pdb")
#K55
weighted_mean_abs_ddG_K55<-Get_weighted_mean_abs_ddG(ddG="./DATA/weights_Binding_K55.txt",
assay_sele = "K55")
Weighted_mean_ddG_structure_fromweighteddata(weighted_mean_ddG=weighted_mean_abs_ddG_K55,
input_PDB = "./DATA/pdb5o2t.ent",
chain_KRAS = "A",
output_PDB_file="./DATA/figure5C_K55_binding_ab_ddG_5o2t.pdb")
#to make figure5b, use chimeraX. key:color bfactor sel range -2,2
#5c
#to make figure5c, use chimeraX. key:color sel gray
#binding interface of binding partners
figure5B<-Get_bindingresidue_bindingpartners()
# paste0(figure5B[binding_partner=="RAF"&scHAmin_ligand<5,Pos],collapse=",")
# paste0(figure5B[binding_partner=="PI3"&scHAmin_ligand<5,Pos],collapse=",")
# paste0(figure5B[binding_partner=="RAL"&scHAmin_ligand<5,Pos],collapse=",")
# #SOS1 chain R
# paste0(figure5B[binding_partner=="SOS1"&scHAmin_ligand<5,Pos],collapse=",")
# #SOS1 chain Q
# paste0(figure5B[binding_partner=="SOS2"&scHAmin_ligand<5,Pos],collapse=",")
# paste0(figure5B[binding_partner=="K27"&scHAmin_ligand<5,Pos],collapse=",")
# paste0(figure5B[binding_partner=="K55"&scHAmin_ligand<5,Pos],collapse=",")
#5d
Plot_ddG_effector_bf_heatmap(ddG1="./DATA/weights_Binding_RAF.txt",
assay1="RAF1",
ddG2="./DATA/weights_Binding_PI3.txt",
assay2="PIK3CG",
ddG3="./DATA/weights_Binding_RAL.txt",
assay3="RALGDS",
anno=anno_final3,
bind1=scHAmin_ligand_RAF,
bind2=scHAmin_ligand_PI3,
bind3=scHAmin_ligand_RAL)
######
#figure 6
######
#6a
all_allosteric_site_list<-Plot_major_allosteric_site_combined_threshold(ddG1="./DATA/weights_Binding_RAF.txt",
assay1="RAF",
ddG2="./DATA/weights_Binding_PI3.txt",
assay2="PI3",
ddG3="./DATA/weights_Binding_RAL.txt",
assay3="RAL",
ddG4="./DATA/weights_Binding_SOS.txt",
assay4="SOS",
ddG5="./DATA/weights_Binding_K27.txt",
assay5="K27",
ddG6="./DATA/weights_Binding_K55.txt",
assay6="K55",
anno=anno_final3,
allosteric_list = all_allosteric_site_list,
rect_input=rects)
all_allosteric_site_list[["p"]]
#6b
Plot_ddG_all_allosteric_heatmap(ddG1="./DATA/weights_Binding_RAF.txt",
assay1="RAF1",
ddG2="./DATA/weights_Binding_PI3.txt",
assay2="PIK3CG",
ddG3="./DATA/weights_Binding_RAL.txt",
assay3="RALGDS",
ddG4="./DATA/weights_Binding_SOS.txt",
assay4="SOS1",
ddG5="./DATA/weights_Binding_K27.txt",
assay5="DARPin K27",
ddG6="./DATA/weights_Binding_K55.txt",
assay6="DARPin K55",
anno=anno_final3,
list1 = all_allosteric_site_list[["RAF"]],
list2 = all_allosteric_site_list[["PI3"]],
list3 = all_allosteric_site_list[["RAL"]],
list4 = all_allosteric_site_list[["SOS"]],
list5 = all_allosteric_site_list[["K27"]],
list6 = all_allosteric_site_list[["K55"]]
)
######
#ED figure 1
######
#S1a, b
Plot_fitness_correlation_blocks(stability_nor_df,"Abundance")
Plot_fitness_correlation_blocks(RAF_nor_df,"RAF1 binding")
#S1c
Plot_kuriyan_cor(kuriyan_list="./DATA/kuriyan_list.RData")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1C_kuriyan_fitness_cor.pdf", device = cairo_pdf,height = 40,width=40,units = "mm")
#S1d
Plot_cor_gr_tecan_binding(tecandata = "/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/invitro validation tecan 0615/20230616_tecanA_1.txt",
plasmidid = "/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/invitro validation tecan 0615/plasmid_plate_0615.csv",
single = all_data_pos[Nham_aa<=1,])
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1D_tecantest_fitness_cor.pdf", device = cairo_pdf,height = 40,width=40,units = "mm")
#S1e
Plot_distribution_fitness(input=all_data_pos,assay_name = "RAF",anno_input = anno_final3)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1E_distribution_fitness_cor.pdf", device = cairo_pdf,height = 20,width=80,units = "mm")
#S1f
Folding_pre_ob_fitness<-Merge_ddGf_fitness(prediction="./DATA/predicted_phenotypes_all.txt",
folding="./DATA/weights_Folding.txt",
block1_dimsum_df = "./DATA/CW_RAS_abundance_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "./DATA/CW_RAS_abundance_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "./DATA/CW_RAS_abundance_3_fitness_replicates_fullseq.RData",
wt_aa_input=wt_aa)
Plot2d_ddGf_fitness(pre_nor = Folding_pre_ob_fitness,
fold_n=1,
mochi_parameters = "./DATA/linears_weights_Abundance1.txt",
phenotypen = 1,RT=0.001987*(273+30),bin_input = 50)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1f1_block1_ddGf_fitness.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot2d_ddGf_fitness(pre_nor = Folding_pre_ob_fitness,
fold_n=1,
mochi_parameters = "./DATA/linears_weights_Abundance2.txt",
phenotypen = 2,RT=0.001987*(273+30),bin_input = 50)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1f2_block2_ddGf_fitness.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot2d_ddGf_fitness(pre_nor = Folding_pre_ob_fitness,
fold_n=1,
mochi_parameters = "./DATA/linears_weights_Abundance3.txt",
phenotypen = 3,RT=0.001987*(273+30),bin_input = 50)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1f3_block3_ddGf_fitness.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
#S1g
Plot2d_ddGf_ob_pre_fitness_perblock(pre_nor = Folding_pre_ob_fitness,phenotypen = 1)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1g1_block1_pre_ob_fitness.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot2d_ddGf_ob_pre_fitness_perblock(pre_nor = Folding_pre_ob_fitness,phenotypen = 2)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1g2_block2_pre_ob_fitness.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot2d_ddGf_ob_pre_fitness_perblock(pre_nor = Folding_pre_ob_fitness,phenotypen = 3)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1g3_block3_pre_ob_fitness.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
#S1h
Plot_pre_12_ob_3_fitness_heldout_cor(prediction="/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/predicted_phenotypes_all.txt",
observed="/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/predicted_phenotypes_all.txt",
phenotypen=1)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1h1_block1_pre12_ob3_fitness_heldout.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot_pre_12_ob_3_fitness_heldout_cor(prediction="/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/predicted_phenotypes_all.txt",
observed="/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/predicted_phenotypes_all.txt",
phenotypen=2)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1h2_block2_pre12_ob3_fitness_heldout.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot_pre_12_ob_3_fitness_heldout_cor(prediction="/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/predicted_phenotypes_all.txt",
observed="/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/predicted_phenotypes_all.txt",
phenotypen=3)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1h3_block3_pre12_ob3_fitness_heldout.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
#S1i
RAF_pre_ob_fitness<-Merge_ddGb_ob_pre_fitness(prediction="/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/predicted_phenotypes_all.txt",
block1_dimsum_df = "/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/CW_RAS_abundance_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/CW_RAS_abundance_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/CW_RAS_abundance_3_fitness_replicates_fullseq.RData",
assay_sele="RAF1",
wt_aa_input=wt_aa)
Plot3d_ddGf_ddGb_ob_pre_fitness(binding_input=RAF_pre_ob_fitness,
folding_assay = Abundance1,
binding_assay = Binding1_RAF,
RT=0.001987*(273+30),
mochi_parameters = "./DATA/linears_weights_Binding1_RAF.txt")
Plot3d_ddGf_ddGb_ob_pre_fitness(binding_input=RAF_pre_ob_fitness,
folding_assay = Abundance2,
binding_assay = Binding2_RAF,
RT=0.001987*(273+30),
mochi_parameters = "./DATA/linears_weights_Binding2_RAF.txt")
Plot3d_ddGf_ddGb_ob_pre_fitness(binding_input=RAF_pre_ob_fitness,
folding_assay = Abundance3,
binding_assay = Binding3_RAF,
RT=0.001987*(273+30),
mochi_parameters = "./DATA/linears_weights_Binding3_RAF.txt")
#S1j
Plot2d_ddGf_ob_pre_fitness_perblock(pre_nor = RAF_pre_ob_fitness,phenotypen = 13)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1j1_block1_pre_ob_fitness.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot2d_ddGf_ob_pre_fitness_perblock(pre_nor = RAF_pre_ob_fitness,phenotypen = 14)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1j2_block2_pre_ob_fitness.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot2d_ddGf_ob_pre_fitness_perblock(pre_nor = RAF_pre_ob_fitness,phenotypen = 15)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1j3_block3_pre_ob_fitness.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
#S1k
Plot_pre_12_ob_3_fitness_heldout_cor(prediction="/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/predicted_phenotypes_all.txt",
observed="./DATA/predicted_phenotypes_all.txt",
phenotypen=13)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1k1_block1_pre12_ob3_fitness_heldout.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot_pre_12_ob_3_fitness_heldout_cor(prediction="/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/predicted_phenotypes_all.txt",
observed="./DATA/predicted_phenotypes_all.txt",
phenotypen=14)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1k2_block2_pre12_ob3_fitness_heldout.pdf", device = cairo_pdf,height = 35,width=70,units = "mm")
Plot_pre_12_ob_3_fitness_heldout_cor(prediction="/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/predicted_phenotypes_all.txt",
observed="./DATA/predicted_phenotypes_all.txt",
phenotypen=15)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS1k3_block3_pre12_ob3_fitness_heldout.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
######
#ED figure 2
######
#S2a
Plot_beta_strand_propagation_heattmap(ddG="./DATA/weights_Binding_RAF.txt",
assay_sele = "RAF")+theme(strip.text.x = element_text(margin = margin(t = 0.4,0,b = 0.2,0, "mm")),
strip.text = element_text(size=5))+
coord_fixed(ratio=2)
#S2b
Plot_ddG_ss(ddG="./DATA/weights_Binding_RAF.txt",
anno=anno_final3,
assay_sele="RAF",
rect_input=rects,
rect_alpha=rects_alpha_all)
#test
Plot_fisher_test(target_group1="b1",
other_group2="others",
condition1="allosteric",
condition2="others",
g1c1 = 29,
g1c2 = 142,
g2c1 = 363-29,
g2c2 = 2712-142,
x_y = c("ddG", "structure"))
#test secondary structures one by one
#S2c
Plot_allosteric_mut_distance_2colors(ddG="./DATA/weights_Binding_RAF.txt",
weighted_mean_ddG=weighted_mean_abs_ddG_RAF,
anno=anno_final3,
assay_sele="RAF",
rect_input=rects)
#S2defg
Sotorasib_dis<-Get_sotorasib_pocket(input_file = "./DATA/pdb6oim.ent")
ggarrange(
Plot_allosteric_ddG_dis_pocket_color(ddG="./DATA/weights_Binding_RAF.txt",
anno=anno_final3,
pocket_anno=final_distance_dc_anno_for_anno_mt_5,
pocket = "pocket1",
assay_sele="RAF",
pocket2=Sotorasib_dis),
Plot_allosteric_ddG_dis_pocket_color(ddG="./DATA/weights_Binding_RAF.txt",
anno=anno_final3,
pocket_anno=final_distance_dc_anno_for_anno_mt_5,
pocket = "pocket2",
assay_sele="RAF",
pocket2=Sotorasib_dis),
Plot_allosteric_ddG_dis_pocket_color(ddG="./DATA/weights_Binding_RAF.txt",
anno=anno_final3,
pocket_anno=final_distance_dc_anno_for_anno_mt_5,
pocket = "pocket3",
assay_sele="RAF",
pocket2=Sotorasib_dis),
Plot_allosteric_ddG_dis_pocket_color(ddG="./DATA/weights_Binding_RAF.txt",
anno=anno_final3,
pocket_anno=final_distance_dc_anno_for_anno_mt_5,
pocket = "pocket4",
assay_sele="RAF",
pocket2=Sotorasib_dis),
ncol=1,align="v"
)
#S2h
Plot_cor_gr_tecan_binding_MoCHi_prediction_double(tecandata = "/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/invitro validation tecan 0615/20230616_tecanA_1.txt",
plasmidid = "/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/invitro validation tecan 0615/plasmid_plate_0615.csv",
ddG1 = "/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/weights_Folding.txt",
ddG2 = "/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/weights_Binding_RAF.txt")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS2h_tecantest_doublemutations_cor.pdf", device = cairo_pdf,height = 45,width=45,units = "mm")
######
#ED figure 3
######
#S3a
Plot_fitness_correlation_blocks(PI3_nor_df,"PIK3CG binding")
Plot_fitness_correlation_blocks(RAL_nor_df,"RALGDS binding")
Plot_fitness_correlation_blocks(SOS_nor_df,"SOS1 binding")
Plot_fitness_correlation_blocks(K27_nor_df,"DARPin K27 binding")
Plot_fitness_correlation_blocks(K55_nor_df,"DARPin K55 binding")
#S3b
Plot2d_ddGb_ob_pre_fitness(prediction="./DATA/predicted_phenotypes_all.txt",
block1_dimsum_df = "./DATA/CW_RAS_binding_PI3_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "./DATA/CW_RAS_binding_PI3_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "./DATA/CW_RAS_binding_PI3_3_fitness_replicates_fullseq.RData",
assay_sele = "PIK3CG",
wt_aa_input=wt_aa)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS3b1_PIK3CG_pre_ob_fitness_R2.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot2d_ddGb_ob_pre_fitness(prediction="./DATA/predicted_phenotypes_all.txt",
block1_dimsum_df = "./DATA/CW_RAS_binding_RAL_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "./DATA/CW_RAS_binding_RAL_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "./DATA/CW_RAS_binding_RAL_3_fitness_replicates_fullseq.RData",
assay_sele = "RALGDS",
wt_aa_input=wt_aa)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS3b2_RALGDS_pre_ob_fitness_R2.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot2d_ddGb_ob_pre_fitness(prediction="./DATA/predicted_phenotypes_all.txt",
block1_dimsum_df = "./DATA/CW_RAS_binding_SOS_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "./DATA/CW_RAS_binding_SOS_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "./DATA/CW_RAS_binding_SOS_3_fitness_replicates_fullseq.RData",
assay_sele = "SOS1",
wt_aa_input=wt_aa)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS3b3_SOS1_pre_ob_fitness_R2.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot2d_ddGb_ob_pre_fitness(prediction="./DATA/predicted_phenotypes_all.txt",
block1_dimsum_df = "./DATA/CW_RAS_binding_K27_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "./DATA/CW_RAS_binding_K27_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "./DATA/CW_RAS_binding_K27_3_fitness_replicates_fullseq.RData",
assay_sele = "DARPin K27",
wt_aa_input=wt_aa)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS3b4_K27_pre_ob_fitness_R2.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot2d_ddGb_ob_pre_fitness(prediction="./DATA/predicted_phenotypes_all.txt",
block1_dimsum_df = "./DATA/CW_RAS_binding_K55_1_fitness_replicates_fullseq.RData",
block2_dimsum_df = "./DATA/CW_RAS_binding_K55_2_fitness_replicates_fullseq.RData",
block3_dimsum_df = "./DATA/CW_RAS_binding_K55_3_fitness_replicates_fullseq.RData",
assay_sele = "DARPin K55",
wt_aa_input=wt_aa)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS3b5_K55_pre_ob_fitness_R2.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
#S3c
Plot_pre_12_ob_3_fitness_cor_all_heldout(prediction="/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/predicted_phenotypes_all.txt",
observed="./DATA/predicted_phenotypes_all.txt",
assay_sele = "PIK3CG",
r_y=0.2)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS3C1_PI3_pre_ob_fitness_heldout.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot_pre_12_ob_3_fitness_cor_all_heldout(prediction="/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/predicted_phenotypes_all.txt",
observed="./DATA/predicted_phenotypes_all.txt",
assay_sele = "RALGDS",
r_y=0.2)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS3C2_RALGDS_pre_ob_fitness_heldout.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot_pre_12_ob_3_fitness_cor_all_heldout(prediction="/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/predicted_phenotypes_all.txt",
observed="./DATA/predicted_phenotypes_all.txt",
assay_sele = "SOS1",
r_y=0.2)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS3C3_SOS1_pre_ob_fitness_heldout.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot_pre_12_ob_3_fitness_cor_all_heldout(prediction="/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/predicted_phenotypes_all.txt",
observed="./DATA/predicted_phenotypes_all.txt",
assay_sele = "DARPin K27",
r_y=0.2)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS3C4_K27_pre_ob_fitness_heldout.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
Plot_pre_12_ob_3_fitness_cor_all_heldout(prediction="/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/predicted_phenotypes_all.txt",
observed="./DATA/predicted_phenotypes_all.txt",
assay_sele = "DARPin K55",
r_y=0.2)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS3C5_K55_pre_ob_fitness_heldout.pdf", device = cairo_pdf,height = 35,width=60,units = "mm")
######
#ED figure 4
######
#s4a
Plot_figureS4C_ddG_heatmap_1124(ddG1="./DATA/weights_Folding.txt",
assay1="folding",
ddG2="./DATA/weights_Binding_RAF.txt",
assay2="RAF1",
ddG3="./DATA/weights_Binding_PI3.txt",
assay3="PIK3CG",
ddG4="./DATA/weights_Binding_RAL.txt",
assay4="RALGDS",
ddG5="./DATA/weights_Binding_SOS.txt",
assay5="SOS1",
ddG6="./DATA/weights_Binding_K27.txt",
assay6="DARPin K27",
ddG7="./DATA/weights_Binding_K55.txt",
assay7="DARPin K55")
#s4b
ggarrange(Plot_ROCAUC_ddG_fitness_binding_interface(fitness_all=all_data_pos,
weighted_meab_abs_ddGf=weighted_mean_abs_ddG_fold,
weighted_meab_abs_ddGb=weighted_mean_abs_ddG_PI3,
anno_input=anno_final3,
bind="PI3",
bind_ligand = "scHAmin_ligand_PI3")+ggtitle("PIK3CG"),
Plot_ROCAUC_ddG_fitness_binding_interface(fitness_all=all_data_pos,
weighted_meab_abs_ddGf=weighted_mean_abs_ddG_fold,
weighted_meab_abs_ddGb=weighted_mean_abs_ddG_RAL,
anno_input=anno_final3,
bind="RAL",
bind_ligand = "scHAmin_ligand_RAL")+ggtitle("RALGDS"),
Plot_ROCAUC_ddG_fitness_binding_interface(fitness_all=all_data_pos,
weighted_meab_abs_ddGf=weighted_mean_abs_ddG_fold,
weighted_meab_abs_ddGb=weighted_mean_abs_ddG_K55,
anno_input=anno_final3,
bind="SOS",
bind_ligand = "scHAmin_ligand_SOS")+ggtitle("SOS1"),
Plot_ROCAUC_ddG_fitness_binding_interface(fitness_all=all_data_pos,
weighted_meab_abs_ddGf=weighted_mean_abs_ddG_fold,
weighted_meab_abs_ddGb=weighted_mean_abs_ddG_K27,
anno_input=anno_final3,
bind="K27",
bind_ligand = "scHAmin_ligand_K27")+ggtitle("DARPin K27"),
Plot_ROCAUC_ddG_fitness_binding_interface(fitness_all=all_data_pos,
weighted_meab_abs_ddGf=weighted_mean_abs_ddG_fold,
weighted_meab_abs_ddGb=weighted_mean_abs_ddG_K55,
anno_input=anno_final3,
bind="K55",
bind_ligand = "scHAmin_ligand_K55")+ggtitle("DARPin K55"),
ncol=6
)
######
#ED figure 5
######
Plot_ddG_all_bf_heatmap(ddG1="./DATA/weights_Binding_RAF.txt",
assay1="RAF1",
ddG2="./DATA/weights_Binding_PI3.txt",
assay2="PIK3CG",
ddG3="./DATA/weights_Binding_RAL.txt",
assay3="RALGDS",
ddG4="./DATA/weights_Binding_SOS.txt",
assay4="SOS1",
ddG5="./DATA/weights_Binding_K27.txt",
assay5="DARPin K27",
ddG6="./DATA/weights_Binding_K55.txt",
assay6="DARPin K55",
anno=anno_final3,
bind1=scHAmin_ligand_RAF,
bind2=scHAmin_ligand_PI3,
bind3=scHAmin_ligand_RAL,
bind4=scHAmin_ligand_SOS,
bind5=scHAmin_ligand_K27,
bind6=scHAmin_ligand_K55
)+
theme(strip.background = element_rect(colour="white",fill=NULL,linetype = NULL))
######
#ED figure 6
######
combined_threshold<-Get_combined_threshold(ddG1="./Data/weights_Binding_RAF.txt",
assay1="RAF",
ddG2="./Data/weights_Binding_PI3.txt",
assay2="PI3",
ddG3="./Data/weights_Binding_RAL.txt",
assay3="RAL",
ddG4="./Data/weights_Binding_SOS.txt",
assay4="SOS",
ddG5="./Data/weights_Binding_K27.txt",
assay5="K27",
ddG6="./Data/weights_Binding_K55.txt",
assay6="K55",
anno=anno_final3)
Plot_allosteric_mutations_all(ddG="./Data/weights_Binding_RAF.txt",
anno=anno_final3,
assay_sele ="RAF",
threshold=combined_threshold,
rect_input=rects,
rect_alpha=rects_alpha,y_min=-1.5,y_max=3.2)
Plot_allosteric_mutations_all(ddG="./Data/weights_Binding_PI3.txt",
anno=anno_final3,
assay_sele ="PI3",
threshold=combined_threshold,
rect_input=rects,
rect_alpha=rects_alpha,y_min=-1.5,y_max=3.2)
Plot_allosteric_mutations_all(ddG="./Data/weights_Binding_RAL.txt",
anno=anno_final3,
assay_sele ="RAL",
threshold=combined_threshold,
rect_input=rects,
rect_alpha=rects_alpha,y_min=-1.5,y_max=3.2)
Plot_allosteric_mutations_all(ddG="./Data/weights_Binding_SOS.txt",
anno=anno_final3,
assay_sele ="SOS",
threshold=combined_threshold,
rect_input=rects,
rect_alpha=rects_alpha,y_min=-1.5,y_max=3.2)
Plot_allosteric_mutations_all(ddG="./Data/weights_Binding_K27.txt",
anno=anno_final3,
assay_sele ="K27",
threshold=combined_threshold,
rect_input=rects,
rect_alpha=rects_alpha,y_min=-2.5,y_max=2.5)
Plot_allosteric_mutations_all(ddG="./Data/weights_Binding_K55.txt",
anno=anno_final3,
assay_sele ="K55",
threshold=combined_threshold,
rect_input=rects,
rect_alpha=rects_alpha,y_min=-1.5,y_max=3.2)
######
#ED figure 7
######
Plot_allosteric_mutations_enrichment(ddG="./Data/weights_Binding_RAF.txt",
anno=anno_final3,
assay_sele ="RAF",
threshold=combined_threshold)
Plot_allosteric_mutations_enrichment(ddG="./Data/weights_Binding_PI3.txt",
anno=anno_final3,
assay_sele ="PI3",
threshold=combined_threshold)
Plot_allosteric_mutations_enrichment(ddG="./Data/weights_Binding_RAL.txt",
anno=anno_final3,
assay_sele ="RAL",
threshold=combined_threshold)
Plot_allosteric_mutations_enrichment(ddG="./Data/weights_Binding_SOS.txt",
anno=anno_final3,
assay_sele ="SOS",
threshold=combined_threshold)
Plot_allosteric_mutations_enrichment(ddG="./Data/weights_Binding_K27.txt",
anno=anno_final3,
assay_sele ="K27",
threshold=combined_threshold)
Plot_allosteric_mutations_enrichment(ddG="./Data/weights_Binding_K55.txt",
anno=anno_final3,
assay_sele ="K55",
threshold=combined_threshold)
######
#ED figure 8
######
#a heatmap
Plot_heatmap_fitness_block1(GAP_nor_df_pos)+
theme(axis.text.y = element_text(family="Courier New",angle=90,size=5, vjust =.5,hjust =.5,margin=margin(0,-0.5,0,0,"mm")))
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8a_GAP_block1_fitness.pdf", device = cairo_pdf,height = 120,width=120,units = "mm")
#b fitness correlation
Plot_fitness_correlation_block1(GAP_nor_df_pos)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8b_GAP_block1_fitness_cor.pdf", device = cairo_pdf,height = 60,width=60,units = "mm")
#c growthrate of GAP and RAF
Plot_density_GAP_RAF_single_gr(GAP_fitness = GAP_nor_df_pos,
RAF_fitness = RAF_nor_df_pos,
driven_mt1 = "G12C",
driven_mt2 = "G12D",
driven_mt3 = "G12V")
Plot_density_GAP_RAF_single_gr_6mut(GAP_fitness = GAP_nor_df_pos,
RAF_fitness = RAF_nor_df_pos,
driven_mt1 = "G12C",
driven_mt2 = "G12D",
driven_mt3 = "G12V",
driven_mt4 = "Q61L",
driven_mt5 = "Q61H",
driven_mt6 = "G13D")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8c_GAP_RAF_block1_single_growthrate_density_plot_6mut.pdf", device = cairo_pdf,height = 40,width=150,units = "mm")
# #d G12C vs WT
# Plot_drivenmt_wt_gr(input = GAP_nor_df_pos,
# driven_mt = "G12C",
# colour_r = colour_scheme[["red"]])
# ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8d1_GAP_block1_double_growthrate_G12CWT_cor.pdf", device = cairo_pdf,height = 50,width=50,units = "mm")
# Plot_drivenmt_wt_gr(input = RAF_nor_df_pos[block=="block1",],
# driven_mt = "G12C",
# colour_r = colour_scheme[["blue"]])
# ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8d2_RAF_block1_double_growthrate_G12CWT_cor.pdf", device = cairo_pdf,height = 50,width=50,units = "mm")
# Plot_drivenmt_wt_gr(input = GAP_nor_df_pos,
# driven_mt = "G12D",
# colour_r = colour_scheme[["red"]])
# ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8d1_GAP_block1_double_growthrate_G12DWT_cor.pdf", device = cairo_pdf,height = 50,width=50,units = "mm")
# Plot_drivenmt_wt_gr(input = RAF_nor_df_pos[block=="block1",],
# driven_mt = "G12D",
# colour_r = colour_scheme[["blue"]])
# ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8d2_RAF_block1_double_growthrate_G12DWT_cor.pdf", device = cairo_pdf,height = 50,width=50,units = "mm")
# Plot_drivenmt_wt_gr(input = GAP_nor_df_pos,
# driven_mt = "G12V",
# colour_r = colour_scheme[["red"]])
# ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8d1_GAP_block1_double_growthrate_G12VWT_cor.pdf", device = cairo_pdf,height = 50,width=50,units = "mm")
# Plot_drivenmt_wt_gr(input = RAF_nor_df_pos[block=="block1",],
# driven_mt = "G12V",
# colour_r = colour_scheme[["blue"]])
# ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8d2_RAF_block1_double_growthrate_G12VWT_cor.pdf", device = cairo_pdf,height = 50,width=50,units = "mm")
#
# Plot_drivenmt_wt_fitness(input = GAP_nor_df_pos,
# driven_mt = "G12C")
# d fitness driven mut vs wt
Plot_drivenmt_wt_fitness_color_fig3(input = GAP_nor_df_pos,
driven_mt = "G12C",
ddG_RAFRBD="/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/weights_Binding_RAF.txt",
anno=anno_final3,
assay_sele="RAF")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8d3_GAP_block1_double_fitness_G12CWT_cor.pdf", device = cairo_pdf,height = 50,width=120,units = "mm")
Plot_drivenmt_wt_fitness_color_fig3(input = GAP_nor_df_pos,
driven_mt = "G12D",
ddG_RAFRBD="/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/weights_Binding_RAF.txt",
anno=anno_final3,
assay_sele="RAF")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8d3_GAP_block1_double_fitness_G12DWT_cor.pdf", device = cairo_pdf,height = 50,width=120,units = "mm")
Plot_drivenmt_wt_fitness_color_fig3(input = GAP_nor_df_pos,
driven_mt = "G12V",
ddG_RAFRBD="/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/weights_Binding_RAF.txt",
anno=anno_final3,
assay_sele="RAF")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8d3_GAP_block1_double_fitness_G12VWT_cor.pdf", device = cairo_pdf,height = 50,width=120,units = "mm")
Plot_drivenmt_wt_fitness_color_fig3(input = RAF_nor_df_pos,
driven_mt = "G12C",
ddG_RAFRBD="/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/weights_Binding_RAF.txt",
anno=anno_final3,
assay_sele="RAF")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8d4_RAF_block1_double_fitness_G12CWT_cor.pdf", device = cairo_pdf,height = 50,width=120,units = "mm")
Plot_drivenmt_wt_fitness_color_fig3(input = RAF_nor_df_pos,
driven_mt = "G12D",
ddG_RAFRBD="/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/weights_Binding_RAF.txt",
anno=anno_final3,
assay_sele="RAF")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8d4_RAF_block1_double_fitness_G12DWT_cor.pdf", device = cairo_pdf,height = 50,width=120,units = "mm")
Plot_drivenmt_wt_fitness_color_fig3(input = RAF_nor_df_pos,
driven_mt = "G12V",
ddG_RAFRBD="/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/weights_Binding_RAF.txt",
anno=anno_final3,
assay_sele="RAF")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS8d4_RAF_block1_double_fitness_G12VWT_cor.pdf", device = cairo_pdf,height = 50,width=120,units = "mm")
######
#ED figure 9
######
#a fitness heatmap of block1 of fullRAF1 bindingPCA
Plot_heatmap_fitness_block1(fullRAF_nor_df_pos)+
theme(axis.text.y = element_text(family="Courier New",angle=90,size=5, vjust =.5,hjust =.5,margin=margin(0,-0.5,0,0,"mm")))
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS9a_fullRAF1_block1_fitness.pdf", device = cairo_pdf,height = 120,width=120,units = "mm")
#b fitness correlation across triplicates
Plot_fitness_correlation_block1(fullRAF_nor_df_pos)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS9b_fullRAF1_block1_fitness_cor.pdf", device = cairo_pdf,height = 60,width=60,units = "mm")
#c fitness full RAF1 vs RAF1RBD
Plot_fitness_cor_RAF1_full_RBD(fullRAF_nor_df_pos,RAF_nor_df_pos)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS9c_fullRAF1_RBD_block1_fitness_cor.pdf", device = cairo_pdf,height = 40,width=60,units = "mm")
#d mochi fitting Andre's codes
Plot_ddG_fullRAF_RBD("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/weights_Binding_RAF.txt",
"/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/weights_Binding_FULLRAF.txt",
ci95_1 = 1,
ci95_2 =1)
Plot_ddG_fullRAF_RBD("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/weights_Binding_RAF.txt",
"/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/weights_Binding_FULLRAF.txt",
ci95_1 = 10000,
ci95_2 =10000)
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS9d_fullRAF1_RBD_block1_ddG_cor.pdf", device = cairo_pdf,height = 40,width=60,units = "mm")
#c
Plot_fitness_cor_RAF1_full_RBD_color_fig3(fullRAF_nor_df_pos,RAF_nor_df_pos,
ddG_RAFRBD="/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/weights_Binding_RAF.txt",
anno=anno_final3,
assay_sele="RAF")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS9c_fullRAF1_RBD_block1_fitness_cor_color.pdf", device = cairo_pdf,height = 40,width=120,units = "mm")
#d
Plot_ddG_fullRAF_RBD_color_fig3(ddG1 = "/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/weights_Binding_RAF.txt",
ddG2 = "/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/weights_Binding_FULLRAF.txt",
ddG_RAFRBD = "/Users/cweng/Desktop/Chenchun_KRAS_paper/Github_codes_updating/DATA/weights_Binding_RAF.txt",
anno=anno_final3,
assay_sele="RAF")
ggsave("/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fugures//figureS9d_fullRAF1_RBD_block1_ddG_cor_color.pdf", device = cairo_pdf,height = 40,width=120,units = "mm")
######
#sup table 4
######
abundancePCA <- stability_nor_df[,.(block, aa_seq, Nham_aa, WT, fitness, sigma, growthrate, growthrate_sigma, nor_gr, nor_gr_sigma, nor_fitness, nor_fitness_sigma)]
abundancePCA[,assay:="AbundancePCA"]
rafPCA <- RAF_nor_df[,.(block, aa_seq, Nham_aa, WT, fitness, sigma, growthrate, growthrate_sigma, nor_gr, nor_gr_sigma, nor_fitness, nor_fitness_sigma)]
rafPCA[,assay:="BindingPCA RAF1RBD"]
pi3PCA <- PI3_nor_df[,.(block, aa_seq, Nham_aa, WT, fitness, sigma, growthrate, growthrate_sigma, nor_gr, nor_gr_sigma, nor_fitness, nor_fitness_sigma)]
pi3PCA[,assay:="BindingPCA PIK3CGRBD"]
ralPCA <- RAL_nor_df[,.(block, aa_seq, Nham_aa, WT, fitness, sigma, growthrate, growthrate_sigma, nor_gr, nor_gr_sigma, nor_fitness, nor_fitness_sigma)]
ralPCA[,assay:="BindingPCA RALGDSRBD"]
sos1PCA <- SOS_nor_df[,.(block, aa_seq, Nham_aa, WT, fitness, sigma, growthrate, growthrate_sigma, nor_gr, nor_gr_sigma, nor_fitness, nor_fitness_sigma)]
sos1PCA[,assay:="BindingPCA SOS1"]
k27PCA <- SOS_nor_df[,.(block, aa_seq, Nham_aa, WT, fitness, sigma, growthrate, growthrate_sigma, nor_gr, nor_gr_sigma, nor_fitness, nor_fitness_sigma)]
k27PCA[,assay:="BindingPCA DARPin K27"]
k55PCA <- SOS_nor_df[,.(block, aa_seq, Nham_aa, WT, fitness, sigma, growthrate, growthrate_sigma, nor_gr, nor_gr_sigma, nor_fitness, nor_fitness_sigma)]
k55PCA[,assay:="BindingPCA DARPin K55"]
fullrafPCA <- fullRAF_nor_df[,.(block, aa_seq, Nham_aa, WT, fitness, sigma, growthrate, growthrate_sigma, nor_gr, nor_gr_sigma, nor_fitness, nor_fitness_sigma)]
fullrafPCA[,assay:="BindingPCA full length RAF1"]
rafgapPCA <- GAP_nor_df[,.(block, aa_seq, Nham_aa, WT, fitness, sigma, growthrate, growthrate_sigma, nor_gr, nor_gr_sigma, nor_fitness, nor_fitness_sigma)]
rafgapPCA[,assay:="BindingPCA RAF1RBD coexpression GAP"]
sup_table4 <- rbind(abundancePCA,
rafPCA,
pi3PCA,
ralPCA,
sos1PCA,
k27PCA,
k55PCA,
fullrafPCA,
rafgapPCA)
sup_table4 <- as.data.frame(sup_table4)
write.table(sup_table4,"/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/sup_table/sup_table4_fitness_dimsum_updated.csv",sep = "\t", row.names = FALSE, col.names = TRUE,quote = FALSE)
#copy to excel
######
#sup table 5
######
Write_tables5(ddG1="/Users/cweng/Desktop/KRAS_Mochi_AF_20220906/mochi_model_realb_l2000001/task_1/weights/weights_Folding.txt",
assay1="folding",
ddG2="/Users/cweng/Desktop/KRAS_Mochi_AF_20220906/mochi_model_realb_l2000001/task_1/weights/weights_Binding_RAF.txt",
assay2="RAF1",
ddG3="/Users/cweng/Desktop/KRAS_Mochi_AF_20220906/mochi_model_realb_l2000001/task_1/weights/weights_Binding_PI3.txt",
assay3="PIK3CG",
ddG4="/Users/cweng/Desktop/KRAS_Mochi_AF_20220906/mochi_model_realb_l2000001/task_1/weights/weights_Binding_RAL.txt",
assay4="RALGDS",
ddG5="/Users/cweng/Desktop/KRAS_Mochi_AF_20220906/mochi_model_realb_l2000001/task_1/weights/weights_Binding_SOS.txt",
assay5="SOS1",
ddG6="/Users/cweng/Desktop/KRAS_Mochi_AF_20220906/mochi_model_realb_l2000001/task_1/weights/weights_Binding_K27.txt",
assay6="DARPin K27",
ddG7="/Users/cweng/Desktop/KRAS_Mochi_AF_20220906/mochi_model_realb_l2000001/task_1/weights/weights_Binding_K55.txt",
assay7="DARPin K55",
ddG8 = "/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/fullRAF/Mochi/weights_Binding_FULLRAF.txt",
assay8 = "full length RAF1",
output="/Users/cweng/Desktop/Chenchun_KRAS_paper/revision/sup_table/sup_table5_mochi_output.xlsx")
######
#MAVEdb update
######
stab_MAVE<-Write_MAVEdb_scoretable(input=all_data_pos,assay_sele = "stab")
write.csv(stab_MAVE[block=="block1"],"./MAVEdb/DATA_upload/abundance_block1_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
write.csv(stab_MAVE[block=="block2"],"./MAVEdb/DATA_upload/abundance_block2_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
write.csv(stab_MAVE[block=="block3"],"./MAVEdb/DATA_upload/abundance_block3_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
RAF1RBD_MAVE<-Write_MAVEdb_scoretable(input=all_data_pos,assay_sele = "RAF")
write.csv(RAF1RBD_MAVE[block=="block1"],"./MAVEdb/DATA_upload/binding_RAF1RBD_block1_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
write.csv(RAF1RBD_MAVE[block=="block2"],"./MAVEdb/DATA_upload/binding_RAF1RBD_block2_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
write.csv(RAF1RBD_MAVE[block=="block3"],"./MAVEdb/DATA_upload/binding_RAF1RBD_block3_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
RALGDS_MAVE<-Write_MAVEdb_scoretable(input=all_data_pos,assay_sele = "RAL")
write.csv(RALGDS_MAVE[block=="block1"],"./MAVEdb/DATA_upload/binding_RALGDSRBD_block1_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
write.csv(RALGDS_MAVE[block=="block2"],"./MAVEdb/DATA_upload/binding_RALGDSRBD_block2_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
write.csv(RALGDS_MAVE[block=="block3"],"./MAVEdb/DATA_upload/binding_RALGDSRBD_block3_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
PI3_MAVE<-Write_MAVEdb_scoretable(input=all_data_pos,assay_sele = "PI3")
write.csv(PI3_MAVE[block=="block1"],"./MAVEdb/DATA_upload/binding_PI3KCGRBD_block1_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
write.csv(PI3_MAVE[block=="block2"],"./MAVEdb/DATA_upload/binding_PI3KCGRBD_block2_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
write.csv(PI3_MAVE[block=="block3"],"./MAVEdb/DATA_upload/binding_PI3KCGRBD_block3_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
SOS1_MAVE<-Write_MAVEdb_scoretable(input=all_data_pos,assay_sele = "SOS")
write.csv(SOS1_MAVE[block=="block1"],"./MAVEdb/DATA_upload/binding_SOS1_block1_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
write.csv(SOS1_MAVE[block=="block2"],"./MAVEdb/DATA_upload/binding_SOS1_block2_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
write.csv(SOS1_MAVE[block=="block3"],"./MAVEdb/DATA_upload/binding_SOS1_block3_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
K27_MAVE<-Write_MAVEdb_scoretable(input=all_data_pos,assay_sele = "K27")
write.csv(K27_MAVE[block=="block1"],"./MAVEdb/DATA_upload/binding_K27_block1_fitness_MAVEdb.csv", quote = FALSE,row.names = F)
write.csv(K27_MAVE[block=="block2"],"./MAVEdb/DATA_upload/binding_K27_block2_fitness_MAVEdb.csv", quote = FALSE,row.names = F)