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Rmd 482a63a haiderinam 2021-03-21 wflow_publish(“analysis/alkati_crizotinib_ic50s.Rmd”) 
library(plotly)
Loading required package: ggplot2
Warning: package 'ggplot2' was built under R version 4.0.2

Attaching package: 'plotly'
The following object is masked from 'package:ggplot2':

    last_plot
The following object is masked from 'package:stats':

    filter
The following object is masked from 'package:graphics':

    layout
library(knitr)
library(tictoc)
library(workflowr)
library(VennDiagram)
Loading required package: grid
Loading required package: futile.logger
library(dplyr)

Attaching package: 'dplyr'
The following objects are masked from 'package:stats':

    filter, lag
The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union
library(foreach)
library(doParallel)
Loading required package: iterators
Loading required package: parallel
library(ggplot2)
library(reshape2)
library(RColorBrewer)
library(devtools)
Loading required package: usethis
library(ggsignif)
library(plotly)
library(BiocManager)
Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help

Attaching package: 'BiocManager'
The following object is masked from 'package:devtools':

    install
library(drc)
Loading required package: MASS

Attaching package: 'MASS'
The following object is masked from 'package:dplyr':

    select
The following object is masked from 'package:plotly':

    select

'drc' has been loaded.
Please cite R and 'drc' if used for a publication,
for references type 'citation()' and 'citation('drc')'.

Attaching package: 'drc'
The following objects are masked from 'package:stats':

    gaussian, getInitial
cleanup=theme_bw() +
  theme(plot.title = element_text(hjust=.5),
        panel.grid.major = element_blank(),
        panel.grid.major.y = element_blank(),
        panel.background = element_blank(),
        # axis.line = element_line(color = "black"),
        axis.text = element_text(face="bold",color="black",size="11"),
        text=element_text(size=11,face="bold"),
        axis.title=element_text(face="bold",size="11"))
# rm(list=ls())

# ic50_all=read.csv("../data/alkati_baf3_ic50s_heatmap.csv",header = T,stringsAsFactors = F)
ic50_all=read.csv("data/alkati_baf3_ic50s_heatmap.csv",header = T,stringsAsFactors = F)
ic50_all=ic50_all%>%
  mutate(transgene=case_when(CellLine%in%c("ALK-ATI-2018-1",
                                           "ALK-ATI-2018-2",
                                           "ALK-ATI-2018-3",
                                           "ALK-ATI-2017-1",
                                           "ALK-ATI-2017-2",
                                           "ALK-ATI-2017-3")~"ALKATI",
                             CellLine%in%c("EML4-ALK 2017",
                                           "EML4-ALK 2018")~"EML4ALK",
                             CellLine%in%"BaF3 PIG"~"PIG"))

ic50_all_melt=melt(ic50_all,id.vars = c("Drug","Date","transgene","CellLine","Replicate"),measure.vars =c("X500","X250","X125","X62.5","X31.25","X15.625","X7.8125","X3.90625","X1.953125"),variable.name = "conc" ,value.name = "doseresponse")

ic50_all_melt=ic50_all_melt%>%mutate(conc=as.numeric(gsub("X","",conc)))

ic50_sum_byreplicate=ic50_all_melt%>%
  group_by(Drug,Date,transgene,CellLine,conc)%>%
  summarize(doseresponse_mean=mean(doseresponse),doseresponse_sd=sd(doseresponse))


plotly=
  ggplot(ic50_sum_byreplicate%>%filter(Drug=="crizotinib"),aes(x=conc,y=doseresponse_mean,color=transgene,fill=CellLine,shape=Date))+
  geom_point()+
  geom_line()+
  facet_wrap(~transgene)+
  scale_y_continuous(name="Response")+
  scale_x_continuous(trans = "log10",name="Dose(nM)")+
  cleanup
ggplotly(plotly)
ic50_sum_bydate=ic50_sum_byreplicate%>%
  group_by(Drug,transgene,CellLine,conc)%>%
  summarize(doseresponse_mean_acrossdates=mean(doseresponse_mean),doseresponse_sd_bydate=sd(doseresponse_mean))

###Crizotinib###
ggplot(ic50_sum_bydate%>%filter(Drug=="crizotinib"),aes(x=conc,y=doseresponse_mean_acrossdates,color=transgene,fill=CellLine))+
geom_point()+
geom_line()+
# facet_wrap(~transgene)+
scale_y_continuous(name="Response")+
scale_x_continuous(trans = "log10",name="Dose(nM)")+
cleanup

Version Author Date
1226db9 haiderinam 2021-03-21 
###Brigatinib###
ggplot(ic50_sum_bydate%>%filter(Drug=="brigatinib"),aes(x=conc,y=doseresponse_mean_acrossdates,color=transgene,fill=CellLine))+
geom_point()+
geom_line()+
# facet_wrap(~transgene)+
scale_y_continuous(name="Response")+
scale_x_continuous(trans = "log10",name="Dose(nM)")+
cleanup

Version Author Date
1226db9 haiderinam 2021-03-21 
####Looking at variation of dose responses across ALKATI lines
ggplot(ic50_sum_bydate%>%filter(transgene=="ALKATI",Drug=="crizotinib"),aes(x=conc,y=doseresponse_mean_acrossdates,fill=CellLine))+
geom_point()+
geom_line()+
geom_ribbon(aes(ymin=doseresponse_mean_acrossdates-doseresponse_sd_bydate,ymax=doseresponse_mean_acrossdates+doseresponse_sd_bydate,alpha=.3))+
scale_y_continuous(name="Response")+
scale_x_continuous(trans = "log10",name="Dose(nM)")+
  cleanup+
theme(legend.position = "none")

Version Author Date
1226db9 haiderinam 2021-03-21 
ic50_sum_bydate_byCellLine=ic50_sum_byreplicate%>%
  group_by(Drug,transgene,conc)%>%
  summarize(doseresponse_sd=sd(doseresponse_mean),
            doseresponse_mean=mean(doseresponse_mean))


ggplot(ic50_sum_bydate_byCellLine%>%filter(Drug=="crizotinib"),aes(x=conc,y=doseresponse_mean,fill=transgene))+
  geom_ribbon(aes(ymin=doseresponse_mean-doseresponse_sd,ymax=doseresponse_mean+doseresponse_sd,alpha=.3))+
  geom_line()+
  geom_point(color="black",shape=21,size=3,aes(fill=factor(transgene)))+
  scale_y_continuous(name="Dose Response")+
  scale_x_continuous(trans = "log10",name="Dose (nM)")+
  cleanup+
  scale_fill_brewer(palette="Set2")+
  theme(legend.position = "none")

Version Author Date
1226db9 haiderinam 2021-03-21 
# ggsave("baf3_alkati_criz.pdf",width=3,height=2.5,units="in",useDingbats=F)

ggplot(ic50_sum_bydate_byCellLine%>%filter(Drug=="brigatinib"),aes(x=conc,y=doseresponse_mean,fill=transgene))+
  geom_ribbon(aes(ymin=doseresponse_mean-doseresponse_sd,ymax=doseresponse_mean+doseresponse_sd,alpha=.3))+
  geom_line()+
  geom_point(color="black",shape=21,size=3,aes(fill=factor(transgene)))+
  scale_y_continuous(name="Dose Response")+
  scale_x_continuous(trans = "log10",name="Dose (nM)")+
  cleanup+
  scale_fill_brewer(palette="Set2")+
  theme(legend.position = "none")

Version Author Date
1226db9 haiderinam 2021-03-21 
# ggsave("baf3_alkati_brig.pdf",width=3,height=2.5,units="in",useDingbats=F)

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  grid      stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] drc_3.0-1           MASS_7.3-51.5       BiocManager_1.30.10
 [4] ggsignif_0.6.0      devtools_2.3.0      usethis_1.6.1      
 [7] RColorBrewer_1.1-2  reshape2_1.4.4      doParallel_1.0.15  
[10] iterators_1.0.12    foreach_1.5.0       dplyr_0.8.5        
[13] VennDiagram_1.6.20  futile.logger_1.4.3 tictoc_1.0         
[16] knitr_1.28          plotly_4.9.2.1      ggplot2_3.3.2      
[19] workflowr_1.6.2    

loaded via a namespace (and not attached):
 [1] fs_1.4.1             httr_1.4.1           rprojroot_1.3-2     
 [4] tools_4.0.0          backports_1.1.7      R6_2.4.1            
 [7] lazyeval_0.2.2       colorspace_1.4-1     withr_2.2.0         
[10] tidyselect_1.1.0     prettyunits_1.1.1    processx_3.4.2      
[13] curl_4.3             compiler_4.0.0       git2r_0.27.1        
[16] cli_2.0.2            formatR_1.7          sandwich_2.5-1      
[19] desc_1.2.0           labeling_0.3         scales_1.1.1        
[22] mvtnorm_1.1-0        callr_3.4.3          stringr_1.4.0       
[25] digest_0.6.25        foreign_0.8-78       rmarkdown_2.1       
[28] rio_0.5.16           pkgconfig_2.0.3      htmltools_0.4.0     
[31] sessioninfo_1.1.1    plotrix_3.7-8        htmlwidgets_1.5.1   
[34] rlang_0.4.6          readxl_1.3.1         farver_2.0.3        
[37] zoo_1.8-8            jsonlite_1.6.1       crosstalk_1.1.0.1   
[40] gtools_3.8.2         zip_2.0.4            car_3.0-7           
[43] magrittr_1.5         Matrix_1.2-18        Rcpp_1.0.4.6        
[46] munsell_0.5.0        fansi_0.4.1          abind_1.4-5         
[49] lifecycle_0.2.0      multcomp_1.4-13      stringi_1.4.6       
[52] whisker_0.4          yaml_2.2.1           carData_3.0-3       
[55] pkgbuild_1.0.8       plyr_1.8.6           promises_1.1.0      
[58] forcats_0.5.0        crayon_1.3.4         lattice_0.20-41     
[61] splines_4.0.0        haven_2.2.0          hms_0.5.3           
[64] ps_1.3.3             pillar_1.4.4         codetools_0.2-16    
[67] pkgload_1.0.2        futile.options_1.0.1 glue_1.4.1          
[70] evaluate_0.14        lambda.r_1.2.4       data.table_1.12.8   
[73] remotes_2.1.1        vctrs_0.3.0          httpuv_1.5.2        
[76] testthat_2.3.2       cellranger_1.1.0     gtable_0.3.0        
[79] purrr_0.3.4          tidyr_1.0.3          assertthat_0.2.1    
[82] xfun_0.13            openxlsx_4.1.5       later_1.0.0         
[85] survival_3.1-12      viridisLite_0.3.0    tibble_3.0.1        
[88] memoise_1.1.0        TH.data_1.0-10       ellipsis_0.3.1