Last updated: 2018-01-10

Code version: 739016a

plot_GTEXres = function(L,pve){
  library(reshape2)
  data_L = melt(L)
  colnames(data_L) = c("tissue","loading","value")
  library(ggplot2)
  tissue_color = as.character(colordata[,2])
  data_L$tissue = factor(data_L$tissue,levels = 1:44 ,labels = as.character(colordata[,1]) )
  data_L$loading = factor(data_L$loading,levels = 1:14 ,labels = paste("loading",1:14,"; pve:", pve[1:14]))
  
  ggplot(data_L,aes(x = tissue,y = value,fill = factor(tissue) )) +
    geom_bar(stat = "identity",width = 0.6) +
    scale_fill_manual(values=tissue_color) +
    scale_x_discrete(labels = NULL) +
    theme_grey()+
    theme(legend.position="right", legend.text=element_text(size=5), axis.text.y = element_text(size = 5)) + 
    labs(title = "GTEx data", y = "loading values" ,x = "tissues", fill="tissue") +
    facet_wrap(~loading, ncol = 2, scales = "free_y") +
    guides(fill = guide_legend(ncol = 1, keyheight = 0.5, keywidth = 0.5))
}
b_flash = readRDS("../data/GTExdata/res_flashr2/bflashvarcol.rds")
load("../data/GTExdata/gtexEQTL_zscore.rds")
ssY = sum(zscore^2)
K = dim(b_flash$EL)[2] -1
pve = (sapply(seq(1,K),function(x){ sum(b_flash$EL[,x]^2 %*% t(b_flash$EF[,x]^2)) }))/ssY
pve = pmax(round(pve,3),0.001)

dat = read.table('../data/GTExColors.txt', sep = '\t', comment.char = '')
colordata = dat[c(1:6,9:18,21:23,26:30,32,33,35,36,38:53),1:2]
L = b_flash$EL[,1:8]
plot_GTEXres(L,pve)

L = b_flash$EL[,9:16]
plot_GTEXres(L,pve)

gsvd = svd(zscore)
pve = (sapply(seq(1,K),function(x){ sum((gsvd$d[x] * gsvd$u[,x] %*% t(gsvd$v[,x]))^2) }))/ssY
pve = pmax(round(pve,3),0.001)
L = gsvd$v[,1:8]
plot_GTEXres(L,pve)

L = gsvd$v[,9:16]
plot_GTEXres(L,pve)

Session information

sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.13.2 (unknown)

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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] reshape2_1.4.2  flashr2_0.4-0   softImpute_1.4  PMA_1.0.9      
 [5] impute_1.48.0   plyr_1.8.4      denoiseR_1.0    Matrix_1.2-11  
 [9] R.matlab_3.6.1  cowplot_0.8.0   ggplot2_2.2.1   ashr_2.2-3     
[13] ebnm_0.1-7      MASS_7.3-47     workflowr_0.4.0 rmarkdown_1.6  

loaded via a namespace (and not attached):
 [1] lattice_0.20-35      Rmosek_7.1.2         colorspace_1.3-2    
 [4] htmltools_0.3.6      yaml_2.1.14          rlang_0.1.2         
 [7] R.oo_1.21.0          withr_2.0.0          R.utils_2.5.0       
[10] REBayes_0.85         foreach_1.4.4        stringr_1.2.0       
[13] munsell_0.4.3        gtable_0.2.0         R.methodsS3_1.7.1   
[16] devtools_1.13.3      codetools_0.2-15     leaps_3.0           
[19] memoise_1.1.0        evaluate_0.10.1      labeling_0.3        
[22] knitr_1.17           pscl_1.5.2           doParallel_1.0.11   
[25] irlba_2.2.1          parallel_3.3.0       curl_2.8.1          
[28] Rcpp_0.12.14         flashClust_1.01-2    scales_0.4.1        
[31] backports_1.1.0      scatterplot3d_0.3-40 truncnorm_1.0-7     
[34] gridExtra_2.3        digest_0.6.12        stringi_1.1.5       
[37] grid_3.3.0           rprojroot_1.2        tools_3.3.0         
[40] magrittr_1.5         lazyeval_0.2.0       tibble_1.3.3        
[43] cluster_2.0.6        FactoMineR_1.36      SQUAREM_2017.10-1   
[46] assertthat_0.2.0     httr_1.3.0           rstudioapi_0.6      
[49] iterators_1.0.9      R6_2.2.2             git2r_0.19.0

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