ALK_ExonImbalance_SKCM_Analysis

Last updated: 2019-02-19

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library(knitr)
library(tictoc)
library(workflowr)

This is workflowr version 1.1.1
Run ?workflowr for help getting started

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)
library(ggsignif)
source("code/contab_maker.R")
source("code/alldata_compiler.R")
source("code/quadratic_solver.R")
source("code/mut_excl_genes_generator.R")
source("code/mut_excl_genes_datapoints.R")
source("code/simresults_generator.R")

######################Cleanup for GGPlot2#########################################
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"))

Making ALK Expression the plots:

alkati_merged_data=read.csv("data/all_data.csv")
alkati_merged_data$alkati=0
alkati_merged_data$alkati[alkati_merged_data$Ratio>=10&alkati_merged_data$mRNA_count>=500&alkati_merged_data$RSEM_normalized>=100]=1
alkati_merged_data$alkati=factor(alkati_merged_data$alkati,levels=c("1","0"))

  ggplot(alkati_merged_data,aes(x=mean_RPKM_1.19, y=mean_RPKM_20.29,color=factor(alkati)))+
    geom_abline(size=1)+
    geom_point(size=4)+
    ####Had to add this line to not overplot the alkati datapoint- Haider 1/31/19
    geom_point(data=alkati_merged_data[alkati_merged_data$alkati==1,],aes(x=mean_RPKM_1.19, y=mean_RPKM_20.29,color=factor(alkati)),size=4)+
    scale_x_continuous(trans = "log10",name="Exon 1:19 RPKM",breaks=c(1e-2,1e0,1e2),labels = parse(text = c("10^-2","10^0","10^2")),limits = c(1e-3,1e3))+
    scale_y_continuous(trans = "log10",name="Exon 20:29 RPKM",breaks=c(1e-2,1e0,1e2),labels = parse(text = c("10^-2","10^0","10^2")),limits = c(1e-3,1e3))+
    scale_color_brewer(palette="Set1",name="ALKATI",labels=c("Yes", "No"))+
    cleanup+
    theme(plot.title = element_text(hjust=.5),
          text = element_text(size=24,face = "bold"),
          axis.title = element_text(face="bold",size="24"),
          axis.text=element_text(face="bold",size="24",colour = "black"))+
    theme(legend.key.size = unit(30,"pt"))

Warning: Transformation introduced infinite values in continuous x-axis

Warning: Removed 2 rows containing missing values (geom_point).

# ggsave("output/alkati_skcm_exonimbalance.pdf",width =12 ,height =10 ,units = "in",useDingbats=F)

#Testing if both kinase and ALK expression are different
ks.test(alkati_merged_data$mean_RPKM_1.19,alkati_merged_data$mean_RPKM_20.29)

Warning in ks.test(alkati_merged_data$mean_RPKM_1.19,
alkati_merged_data$mean_RPKM_20.29): p-value will be approximate in the
presence of ties

    Two-sample Kolmogorov-Smirnov test

data:  alkati_merged_data$mean_RPKM_1.19 and alkati_merged_data$mean_RPKM_20.29
D = 0.40456, p-value < 2.2e-16
alternative hypothesis: two-sided

###We observed a significant difference between the distribution for the 20-29 exons and the 1-19 exons The reported p-value was 2-16.

sessionInfo()

R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.3

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] ggsignif_0.4.0      usethis_1.4.0       devtools_2.0.1     
 [4] RColorBrewer_1.1-2  reshape2_1.4.3      ggplot2_3.1.0      
 [7] doParallel_1.0.14   iterators_1.0.10    foreach_1.4.4      
[10] dplyr_0.7.8         VennDiagram_1.6.20  futile.logger_1.4.3
[13] workflowr_1.1.1     tictoc_1.0          knitr_1.21         

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5     xfun_0.4             remotes_2.0.2       
 [4] purrr_0.3.0          colorspace_1.4-0     htmltools_0.3.6     
 [7] yaml_2.2.0           rlang_0.3.1          pkgbuild_1.0.2      
[10] R.oo_1.22.0          pillar_1.3.1         glue_1.3.0          
[13] withr_2.1.2          R.utils_2.7.0        sessioninfo_1.1.1   
[16] lambda.r_1.2.3       bindrcpp_0.2.2       bindr_0.1.1         
[19] plyr_1.8.4           stringr_1.3.1        munsell_0.5.0       
[22] gtable_0.2.0         R.methodsS3_1.7.1    codetools_0.2-16    
[25] evaluate_0.12        memoise_1.1.0        callr_3.1.1         
[28] ps_1.3.0             Rcpp_1.0.0           backports_1.1.3     
[31] scales_1.0.0         formatR_1.5          desc_1.2.0          
[34] pkgload_1.0.2        fs_1.2.6             digest_0.6.18       
[37] stringi_1.2.4        processx_3.2.1       rprojroot_1.3-2     
[40] cli_1.0.1            tools_3.5.2          magrittr_1.5        
[43] lazyeval_0.2.1       tibble_2.0.1         futile.options_1.0.1
[46] crayon_1.3.4         whisker_0.3-2        pkgconfig_2.0.2     
[49] prettyunits_1.0.2    assertthat_0.2.0     rmarkdown_1.11      
[52] rstudioapi_0.9.0     R6_2.3.0             git2r_0.24.0        
[55] compiler_3.5.2      

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