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Rmd | f8e2d5e | haiderinam | 2019-02-17 | Published Analysis on ALK expression levels #2 |
library(knitr)
library(tictoc)
library(workflowr)
This is workflowr version 1.3.0
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("output/all_data_skcm.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=11,face = "bold"),
axis.title = element_text(face="bold",size="11"),
axis.text=element_text(face="bold",size="11",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).
Version | Author | Date |
---|---|---|
dfdb600 | haiderinam | 2019-02-17 |
# 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.
###The p-value from a Chi-sq test was 2.2e-16 too
#for all ALK data, not ALKATI
ov_expr_obs=c(sum(as.numeric(alkati_merged_data$Ratio20.29>1),na.rm = T),
dim(alkati_merged_data)[1]-sum(as.numeric(alkati_merged_data$Ratio20.29>1),na.rm = T))
ov_expr_expected=c(round(dim(alkati_merged_data)[1]/2),
round(dim(alkati_merged_data)[1]/2))
overexpression=data.frame(rbind(ov_expr_obs,ov_expr_expected))
# overexpression=data.frame(rbind(c(338,13),c(176,176)))
colnames(overexpression)=c("Yes","No")
chisq.test(overexpression)
Pearson's Chi-squared test with Yates' continuity correction
data: overexpression
X-squared = 189.29, df = 1, p-value < 2.2e-16
sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5
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_0.5.0 usethis_1.5.0 devtools_2.0.2
[4] RColorBrewer_1.1-2 reshape2_1.4.3 ggplot2_3.1.1
[7] doParallel_1.0.14 iterators_1.0.10 foreach_1.4.4
[10] dplyr_0.8.1 VennDiagram_1.6.20 futile.logger_1.4.3
[13] workflowr_1.3.0 tictoc_1.0 knitr_1.23
loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 xfun_0.7 remotes_2.0.4
[4] purrr_0.3.2 colorspace_1.4-1 htmltools_0.3.6
[7] yaml_2.2.0 rlang_0.3.4 pkgbuild_1.0.3
[10] pillar_1.4.0 glue_1.3.1 withr_2.1.2
[13] lambda.r_1.2.3 sessioninfo_1.1.1 plyr_1.8.4
[16] stringr_1.4.0 munsell_0.5.0 gtable_0.3.0
[19] codetools_0.2-16 evaluate_0.13 memoise_1.1.0
[22] callr_3.2.0 ps_1.3.0 Rcpp_1.0.1
[25] scales_1.0.0 backports_1.1.4 formatR_1.6
[28] desc_1.2.0 pkgload_1.0.2 fs_1.3.1
[31] digest_0.6.19 stringi_1.4.3 processx_3.3.1
[34] rprojroot_1.3-2 cli_1.1.0 tools_3.5.2
[37] magrittr_1.5 lazyeval_0.2.2 tibble_2.1.1
[40] futile.options_1.0.1 crayon_1.3.4 whisker_0.3-2
[43] pkgconfig_2.0.2 prettyunits_1.0.2 assertthat_0.2.1
[46] rmarkdown_1.12 R6_2.4.0 git2r_0.25.2
[49] compiler_3.5.2