Last updated: 2023-08-30
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Knit directory: duplex_sequencing_screen/
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Unstaged changes:
Modified: .DS_Store
Modified: analysis/ABL_cosmic_analysis.Rmd
Modified: analysis/ABL_kinasefunction_data_parser.Rmd
Modified: analysis/index.Rmd
Modified: code/compare_screens.R
Modified: data/.DS_Store
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Modified: output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/cross-replicate/.DS_Store
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were
made to the R Markdown (analysis/ABL_cosmic_analysis.Rmd
)
and HTML (docs/ABL_cosmic_analysis.html
) files. If you’ve
configured a remote Git repository (see ?wflow_git_remote
),
click on the hyperlinks in the table below to view the files as they
were in that past version.
File | Version | Author | Date | Message |
---|---|---|---|---|
Rmd | f9eea37 | haiderinam | 2023-08-30 | 2023 Updates |
html | f9eea37 | haiderinam | 2023-08-30 | 2023 Updates |
Rmd | 60b906b | haiderinam | 2023-04-10 | Added ROC analyses on BE-SM data |
Rmd | 6b51aa2 | haiderinam | 2023-03-25 | Added Lane 18 Data with ABL Region 1 SM Screen |
Rmd | 81a5af3 | haiderinam | 2023-02-25 | Added shortest codon finder function |
html | 81a5af3 | haiderinam | 2023-02-25 | Added shortest codon finder function |
For the density plots:
library(viridisLite)
library("MASS")
Warning: package 'MASS' was built under R version 4.0.5
Attaching package: 'MASS'
The following object is masked from 'package:plotly':
select
The following object is masked from 'package:dplyr':
select
theme_set(theme_bw(base_size = 16))
# Get density of points in 2 dimensions.
# @param x A numeric vector.
# @param y A numeric vector.
# @param n Create a square n by n grid to compute density.
# @return The density within each square.
get_density <- function(x, y, ...) {
dens <- MASS::kde2d(x, y, ...)
ix <- findInterval(x, dens$x)
iy <- findInterval(y, dens$y)
ii <- cbind(ix, iy)
return(dens$z[ii])
}
set.seed(1)
dat <- data.frame(
x = c(
rnorm(1e4, mean = 0, sd = 0.1),
rnorm(1e3, mean = 0, sd = 0.1)
),
y = c(
rnorm(1e4, mean = 0, sd = 0.1),
rnorm(1e3, mean = 0.1, sd = 0.2)
)
)
This piece of code picks up some of the analysis done in ABL_unevenness_analysis.Rmd
Seeing how well our imatinib resistance mutants work with cosmic mutants
# source("code")
source("code/res_residues_adder.R")
source("code/variants_parser.R")
source("code/compare_samples.R")
source("code/resmuts_adder.R")
source("code/cosmic_data_adder.R")
data=read.csv("output/ABLEnrichmentScreens/Imatinib_Enrichment_2.20.23_v2.csv",header = T,stringsAsFactors = F)
data=read.csv("output/ABLEnrichmentScreens/Imat_Enrichment_bgmerged_2.22.23.csv",header = T,stringsAsFactors = F)
# class(data)
data=res_residues_adder(data)
data=cosmic_data_adder(data)
# data=data%>%rowwise()%>%mutate(netgr_mean=mean(netgr_obs.x,netgr_obs.y))
data=data%>%rowwise()%>%mutate(netgr_mean=mean(netgr_obs_screen1,netgr_obs_screen2))
data$resmut_cosmic="neither"
data[data$cosmic_present%in%TRUE,"resmut_cosmic"]="cosmic"
data[data$resmuts%in%TRUE,"resmut_cosmic"]="resmut"
data$resmut_cosmic=factor(data$resmut_cosmic,levels=c("neither","cosmic","resmut"))
ggplot(data%>%filter(protein_start>=242,protein_start<=494),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+guides(fill = guide_legend(title = "Clinically\n Observed \n Resmut"))+scale_fill_manual(values=c("gray","orange","red"))
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+guides(fill = guide_legend(title = "Clinically\n Observed \n Resmut"))+scale_fill_manual(values=c("gray","orange","red"))
plotly=ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+guides(fill = guide_legend(title = "Cosmic\n Observed \n Mutant"))+scale_fill_manual(values=c("gray","orange","red"))
ggplotly(plotly)
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=score_screen1,y=score_screen2))+
geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
geom_abline()+
scale_x_continuous(name="Score D0 D2")+
scale_y_continuous(name="Score D0 D4")+
labs(fill="Cosmic\n Mutant")+
scale_fill_manual(values=c("gray90","orange","red"))
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=resmut_cosmic,y=score_mean))+geom_boxplot(aes(fill=resmut_cosmic))+scale_fill_manual(values=c("gray90","orange","red"))
# a=data%>%filter(score_mean%in%c(NA,NaN))
# a=data_cosmic%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,score_mean>=0,cosmic_present%in%T)
Netgr Plots for putting in presentation
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-netgr_mean),y=netgr_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name=bquote('Net Growth Rate '(Hours^-1)))+scale_x_discrete(name="Mutant")+scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+cleanup+theme(legend.position = "none")
# ggsave("ImatinibEnrichment_Netgr_Distribution.pdf",width=8,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,score_mean>=0),aes(x=reorder(species,-netgr_mean),y=netgr_mean,fill=resmut_cosmic))+geom_col()+
scale_y_continuous(name=bquote('Net Growth Rate '(Hours^-1)))+
scale_x_discrete(name="Mutant")+
scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+
theme(axis.text.x=element_text(angle=90, hjust=1),
axis.text=element_text(size=6),
panel.grid.major = element_blank(),
panel.grid.major.y = element_blank(),
panel.background = element_blank())+
theme(legend.position = "none")
# ggsave("ImatinibEnrichment_Netgr_Distribution_zoom.pdf",width=6,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494),aes(x=netgr_obs_screen1,y=netgr_obs_screen2))+
geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
geom_abline()+
scale_x_continuous(name="Net Growth Rate D0 D2")+
scale_y_continuous(name="Net Growth Rate D0 D4")+
labs(fill="Sanger\n Mutant")+
scale_fill_manual(values=c("gray90","orange","red"))+
cleanup+theme(legend.position = "none")
# ggsave("ImatinibEnrichment_Plot_netgr_2.21.23.pdf",width=4,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(!species%in%"T315I",protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=resmut_cosmic,y=netgr_mean,fill=resmut_cosmic))+
geom_violin(color="black")+
geom_boxplot(color="black",width=.1)+
# geom_boxplot(color="black")+
scale_fill_manual(values=c("gray90","orange","red"))+scale_y_continuous(name=bquote('Net Growth Rate '(Hours^-1)))+scale_x_discrete("Resistance Status",labels=c("Never\n Seen","Sanger","Known\nResistant"))+cleanup+theme(legend.position = "none")
# ggsave("ImatinibEnrichment_netgr_BoxPlot_2.21.23.pdf",width=4,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-netgr_mean),y=netgr_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+guides(fill = guide_legend(title = "Clinically\n Observed \n Resmut"))+scale_fill_manual(values=c("gray","orange","red"))
#
ggplot(data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494),aes(x=netgr_obs_screen1,y=netgr_obs_screen2))+
geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
geom_abline()+
scale_x_continuous(name="Net Growth Rate D0 D2")+
scale_y_continuous(name="Net Growth Rate D0 D4")+
labs(fill="Sanger\n Mutant")+
scale_fill_manual(values=c("gray90","orange","red"))+
theme(legend.position = "none")
Score plots for putting in presentation
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+cleanup+theme(legend.position = "none")
# ggsave("ImatinibEnrichment_Distribution.pdf",width=8,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,score_mean>=0),aes(x=reorder(species,-score_mean),y=score_mean,fill=resmut_cosmic))+geom_col()+
scale_y_continuous(name="Enrichcment Score")+
scale_x_discrete(name="Mutant")+
scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+
theme(axis.text.x=element_text(angle=90, hjust=1),
axis.text=element_text(size=6),
panel.grid.major = element_blank(),
panel.grid.major.y = element_blank(),
panel.background = element_blank())+
theme(legend.position = "none")
# ggsave("ImatinibEnrichment_Distribution_zoom.pdf",width=6,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(!ct_screen1_after%in%.5,!ct_screen2_after%in%.5,protein_start>=242,protein_start<=494),aes(x=score_screen1,y=score_screen2))+
geom_point(color="black",shape=21,aes(fill=resmut_cosmic))+
geom_abline()+
scale_x_continuous(name="Enrichment Score D0 D2")+
scale_y_continuous(name="Enrichment Score D0 D4")+
labs(fill="Sanger\n Mutant")+
scale_fill_manual(values=c("gray90","orange","red"))+
cleanup+theme(legend.position = "none")
# ggsave("ImatinibEnrichment_Plot_2.21.23.pdf",width=4,height=4,units="in",useDingbats=F)
ggplot(data%>%filter(!species%in%"T315I",protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=resmut_cosmic,y=score_mean,fill=resmut_cosmic))+
geom_violin(color="black")+
geom_boxplot(color="black",width=.1)+
# geom_boxplot(color="black")+
scale_fill_manual(values=c("gray90","orange","red"))+theme(legend.position = "none")+scale_y_continuous("Enrichment Score")+scale_x_discrete("Resistance Status",labels=c("Never\n Seen","Sanger","Known\nResistant"))
# ggsave("ImatinibEnrichment_BoxPlot_2.21.23.pdf",width=4,height=4,units="in",useDingbats=F)
# a=data%>%filter(protein_start>=242,protein_start<=494)
# a=data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1)
# b=a[order(a$score_mean,decreasing=TRUE),]
# b=b[c(1:200),]
# c=a%>%filter(!resmut_cosmic%in%"neither")
#The following function finds the shortest and the likeliest codon given a ref codon and an ALT amino acid
# codon_table
# inputs:
ref_codon="AAT"
alt_aa="A"
#outputs:
#shortest codon nucleotides
#shortest alt codn
codon_table=read.csv("data/codon_table.csv",header = T,stringsAsFactors = F)
mut_probs=read.csv("data/MutationProbabilities/Input_Mutsubmat_broadExac.csv",header = T,stringsAsFactors = F)
mut_probs=mut_probs%>%mutate(subs=paste(ref,">",var,sep = ""))
mut_probs_simple=mut_probs%>%dplyr::select(subs,prop)
shortest_codon_finder=function(ref_codon,alt_aa){
# For a given reference codon and a given ALT residue, this function will find the shortest possible ALT codon. If multiple codons are available
#What is the twist codon for the given alt amino acid?
# twist_codons=codon_table%>%filter(Twist%in%T)
# twist_alt_codon=twist_codons[twist_codons$Letter%in%alt_aa,"Codon"]
#Calculating hamming distance
#Below, I calculate hamming distance by looking for a mismatch between the REF codon and the alt codon at each one of the 3 positions of the codon and adding them up.
# alt_codons=codon_table%>%
# filter(Letter%in%alt_aa)%>%
# rowwise()%>%
# mutate(distance=as.numeric(!substr(ref_codon,1,1)%in%substr(Codon,1,1))+
# as.numeric(!substr(ref_codon,2,2)%in%substr(Codon,2,2))+
# as.numeric(!substr(ref_codon,3,3)%in%substr(Codon,3,3)),
# substitutions=)%>%
# ungroup()
alt_codons=codon_table%>%
filter(Letter%in%alt_aa)%>%
rowwise()%>%
mutate(distance=as.numeric(!substr(ref_codon,1,1)%in%substr(Codon,1,1))+
as.numeric(!substr(ref_codon,2,2)%in%substr(Codon,2,2))+
as.numeric(!substr(ref_codon,3,3)%in%substr(Codon,3,3)),
subs_1=case_when(!substr(ref_codon,1,1)%in%substr(Codon,1,1)~paste(substr(ref_codon,1,1),">",substr(Codon,1,1),sep = ""),
T~""),
subs_2=case_when(!substr(ref_codon,2,2)%in%substr(Codon,2,2)~paste(substr(ref_codon,2,2),">",substr(Codon,2,2),sep = ""),
T~""),
subs_3=case_when(!substr(ref_codon,3,3)%in%substr(Codon,3,3)~paste(substr(ref_codon,3,3),">",substr(Codon,3,3),sep = ""),
T~""))%>%
ungroup()
# alt_codons=alt_codons%>%mutate(
# prob_1=
# )
# mut_probs_simple=mut_probs%>%dplyr::select(subs_1=subs,prop_1=prop)
a=mut_probs_simple
alt_codons=merge(alt_codons,a,by.x="subs_1",by.y="subs",all.x = T,)
alt_codons=merge(alt_codons,a,by.x="subs_2",by.y="subs",all.x = T)
alt_codons=merge(alt_codons,a,by.x="subs_3",by.y="subs",all.x = T)
alt_codons=alt_codons%>%mutate(prop_1=prop,prop_2=prop.x,prop_3=prop.y)%>%dplyr::select(-c("prop","prop.x","prop.y"))
# if alt codon is a 3 nucleotide variant, then
alt_codons[alt_codons$prop_1%in%NA,"prop_1"]=1
alt_codons[alt_codons$prop_2%in%NA,"prop_2"]=1
alt_codons[alt_codons$prop_3%in%NA,"prop_3"]=1
alt_codons=alt_codons%>%mutate(prob=prop_1*prop_2*prop_3)
#################Choosing the shortest ALT codon ###############
#################Method 1: Choose based on shortest hamming distance###############
# #Sorting through the shortest hamming distance
# mindist=min(alt_codons$distance)
# alt_codons=alt_codons%>%filter(distance==mindist)
# #If there are multiple rows at the shortest distance, and one of the codons is the twist codon, choose the twist codon. Aka if no codon is shorter than twist, choose twist
# #Otherwise if there are multiple shortest codons and none of them are the twist codon, then return both of them
# if(sum(as.numeric(alt_codons$Twist%in%T))!=0){
# #The above boolean is saying "if you find twist codon amongst the shortest codons"
# shortest_alt_codon=as.character(alt_codons[alt_codons$Twist%in%T,"Codon"])
# # shortest_alt_codon=alt_codons$Codon
# # class(shortest_alt_codon)
# } else{
# shortest_alt_codon=alt_codons$Codon[1]
# # Note that when there are multiple options for non-twist shortest ALT codons that code for the same residue, I just pick one of them. This happens for the following:
# # "AGG,CGG"
# # "CTC,TTA,TTG"
# # "CTA,TTA"
# # "AGT,TCT"
# # To view all shortest alt codons, use:
# # shortest_alt_codon=paste(alt_codons$Codon,collapse = ",")
# }
#################Method 2: Choose based on mutation probabilities###############
#Choose the codon that yields the shortest hamming distance and the highest probability amongst the shortest codons.
mindist=min(alt_codons$distance)
alt_codons=alt_codons%>%filter(distance==mindist)
alt_codons=alt_codons%>%filter(prob==max(prob))
shortest_alt_codon=alt_codons$Codon
maxprob=alt_codons$prob
#Optional method 3: nother way of choosing shortest codons is to choose the most likeliest codons. This method does chooses the most likeliest codons, even if they're a higher hamming distance away. This is the mutant with the shortest hamming distance in most cases. Sometimes there multiple rows at the shortest hamming distance, so going by probability is fair. For example, two C>T or G>A substitutions are more likely than a single A>T substitution. However, these mutation biases are based on a ABL broad exac dataset with 224 mutations, so I still like the idea of giving higher precedence to hamming distance.
#To execute the optional method 3, comment out the two mindist lines of code
####################################################################
# return(list(shortest_alt_codon))
return(list(shortest_alt_codon,mindist,maxprob))
}
# source("code/shortest_codon_finder.R")
shortest_codon_finder("AAT","A")[[1]][1]
[1] "GCT"
shortest_codon_finder("AAT","A")[[2]][1]
[1] 2
shortest_codon_finder("AAT","A")[[3]][1]
[1] 0.001694037
#The following codon combination is for T315I
shortest_codon_finder("ACT","I")
[[1]]
[1] "ATT"
[[2]]
[1] 1
[[3]]
[1] 0.3928571
#For the following codon combination, there are two non twist shortest codon
shortest_codon_finder("GGG","R")
[[1]]
[1] "AGG"
[[2]]
[1] 1
[[3]]
[1] 0.3035714
library(tictoc)
# tic()
# a=data%>%
# rowwise()%>%
# mutate(alt_codon_shortest=shortest_codon_finder(ref_codon,alt_aa)[[1]][1],
# n_nuc_min=shortest_codon_finder(ref_codon,alt_aa)[[2]][1],
# prob_max=shortest_codon_finder(ref_codon,alt_aa)[[3]][1])
# toc()
# b=a%>%filter(grepl(",",alt_codon_shortest)%in%T)
# unique(b$alt_codon_shortest)
# b=a%>%filter(alt_codon%in%alt_codon_shortest)
# T315I twist ACT to "ATC"
# T315I natural ACT to "ATT"
Are the score non-hits the improbable mutations?
#Among the SNPs in the dataset, what is their nucleotide substitution signature?
#For substitutions with more than 1 possible way of getting a snp, choose the SNP that's more probable in terms of substitution bias
tic()
data=data%>%
rowwise()%>%
mutate(alt_codon_shortest=shortest_codon_finder(ref_codon,alt_aa)[[1]][1],
n_nuc_min=shortest_codon_finder(ref_codon,alt_aa)[[2]][1],
prob_max=shortest_codon_finder(ref_codon,alt_aa)[[3]][1])
toc()
53.171 sec elapsed
data=data%>%mutate(prob_status=case_when(prob_max>=.05&&prob_max<.2~"medium",
prob_max>=.2~"high",
T~"low"))
data$prob_status=factor(data$prob_status,levels=c("low","medium","high"))
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,score_mean>=0),aes(x=reorder(species,-netgr_mean),y=netgr_mean,group=resmut_cosmic,fill=resmut_cosmic,alpha=prob_status))+geom_col()+
scale_y_continuous(name="Net Growth Rate")+
scale_x_discrete(name="Mutant")+
scale_fill_manual(name=c("Resistance Status"),labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+
theme(axis.text.x=element_text(angle=90, hjust=1),
axis.text=element_text(size=6),
panel.grid.major = element_blank(),
panel.grid.major.y = element_blank(),
panel.background = element_blank())
Warning: Using alpha for a discrete variable is not advised.
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=resmut_cosmic,y=prob_max,fill=resmut_cosmic))+
geom_violin(color="black")+
geom_boxplot(color="black",width=.1)+
# geom_boxplot(color="black")+
scale_fill_manual(values=c("gray90","orange","red"))+theme(legend.position = "none")+scale_y_continuous("Enrichment Score")+scale_x_discrete("Resistance Status",labels=c("Never\n Seen","Sanger","Known\nResistant"))
plotly=ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=prob_max,fill=resmut_cosmic))+
geom_density(aes(alpha=.7))
ggplotly(plotly)
a=data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,prob_max>=.2,resmut_cosmic%in%"neither")
mean(a$netgr_mean)
[1] 0.009656468
a=data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,prob_max>=.2,!resmut_cosmic%in%"neither")
# a=data%>%filter(protein_start>=242,protein_start<=494,!resmut_cosmic%in%"neither")
mean(a$netgr_mean)
[1] 0.01258991
# data_snps=data%>%filter(n_nuc_min%in%1,resmut_cosmic%in%"neither")%>%dplyr::select(ref_codon,alt_aa,score_mean)
# a=data%>%filter(!resmut_cosmic%in%"neither")
As it can be seen from the plots, there are a good number of unseen hits that are low probability. However, some resistant mutants are also low probability…
We can imagine that some mutants are scoring higher because of an IL3 independence fitness advantage. Below, I remove the IL3 independence fitness advantage of a mutant. But there are number of mutants that are growing faster under imatinib than under IL3. These starting scoring high.
# dataimat=data
# data=dataimat
datail3=read.csv("output/ABLEnrichmentScreens/IL3_Enrichment_bgmerged_2.20.23.csv",header = T,stringsAsFactors = F)
datail3=datail3%>%rowwise()%>%mutate(netgr_mean=mean(netgr_obs_screen1,netgr_obs_screen2))
# class(data)
# datail3=res_residues_adder(datail3)
# datail3=cosmic_data_adder(datail3)
# # datail3=datail3%>%rowwise()%>%mutate(netgr_mean=mean(netgr_obs.x,netgr_obs.y))
# datail3=datail3%>%rowwise()%>%mutate(netgr_mean=mean(netgr_obs_screen1,netgr_obs_screen2))
# datail3$resmut_cosmic="neither"
# datail3[datail3$cosmic_present%in%TRUE,"resmut_cosmic"]="cosmic"
# datail3[datail3$resmuts%in%TRUE,"resmut_cosmic"]="resmut"
# datail3$resmut_cosmic=factor(datail3$resmut_cosmic,levels=c("neither","cosmic","resmut"))
ggplot(datail3%>%filter(protein_start<=494,protein_start>=242,consequence_terms%in%"missense_variant"),aes(x=netgr_obs_screen1,y=netgr_obs_screen2))+geom_point()+geom_abline()
datail3_simple=datail3%>%dplyr::select(ref_aa,protein_start,alt_aa,netgr_obs_screen1,netgr_obs_screen2,netgr_mean)
data_merged=merge(data,datail3_simple,by=c("ref_aa","protein_start","alt_aa"),suffixes = c("_imat","_il3"))
data_merged=data_merged%>%rowwise()%>%mutate(netgr_adj=.055-(netgr_mean_il3-netgr_mean_imat),
alpha=netgr_mean_il3-netgr_mean_imat)
ggplot(data_merged%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,netgr_mean_il3>=0),aes(x=reorder(species,-netgr_adj),y=netgr_adj,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+cleanup+theme(legend.position = "none")
a=data_merged%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1,netgr_mean_il3>=0)
ggplot(data%>%filter(protein_start>=242,protein_start<=494,n_nuc_min%in%1),aes(x=reorder(species,-netgr_obs_screen2),y=netgr_obs_screen2,fill=resmut_cosmic))+geom_col()+theme(axis.text.x=element_text(angle=90, hjust=1))+scale_y_continuous(name="Enrichcment Score")+scale_x_discrete(name="Mutant")+scale_fill_manual(name="Resistance Status",labels=c("Never Seen","Sanger Mutant","Known Resistant Mutant"),values=c("gray","orange","red"))+cleanup+theme(legend.position = "none")
sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] MASS_7.3-55 viridisLite_0.3.0 RColorBrewer_1.1-2 doParallel_1.0.15
[5] iterators_1.0.12 foreach_1.5.0 tictoc_1.0 plotly_4.9.2.1
[9] ggplot2_3.3.3 dplyr_1.0.6 stringr_1.4.0
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.31 bslib_0.3.1 purrr_0.3.4
[5] colorspace_1.4-1 vctrs_0.3.8 generics_0.0.2 htmltools_0.5.2
[9] yaml_2.2.1 utf8_1.1.4 rlang_0.4.11 jquerylib_0.1.4
[13] later_1.0.0 pillar_1.6.1 glue_1.4.1 withr_2.4.2
[17] DBI_1.1.0 lifecycle_1.0.0 munsell_0.5.0 gtable_0.3.0
[21] workflowr_1.6.2 htmlwidgets_1.5.1 codetools_0.2-16 evaluate_0.14
[25] labeling_0.3 knitr_1.28 fastmap_1.1.0 crosstalk_1.1.0.1
[29] httpuv_1.5.2 fansi_0.4.1 Rcpp_1.0.4.6 promises_1.1.0
[33] backports_1.1.7 scales_1.1.1 jsonlite_1.7.2 farver_2.0.3
[37] fs_1.4.1 digest_0.6.25 stringi_1.7.5 rprojroot_1.3-2
[41] grid_4.0.0 tools_4.0.0 magrittr_2.0.1 sass_0.4.1
[45] lazyeval_0.2.2 tibble_3.1.2 crayon_1.4.1 whisker_0.4
[49] tidyr_1.1.3 pkgconfig_2.0.3 ellipsis_0.3.2 data.table_1.12.8
[53] assertthat_0.2.1 rmarkdown_2.14 httr_1.4.2 R6_2.4.1
[57] git2r_0.27.1 compiler_4.0.0