Last updated: 2020-03-08

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Unstaged changes:
    Modified:   .gitignore
    Modified:   analysis/index.Rmd
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library(corrplot)
corrplot 0.84 loaded
robocov_gtex = get(load("/Users/kushaldey/Documents/Robocov-pages/data/Robocov_Box_all_genes.rda"))
dim(robocov_gtex)
[1]    53    53 16069
robospan = apply(robocov_gtex, 3, sum)/(53*53)
plot(density(robospan), xlab = "Robospan score", ylab = "density")

robospan[order(robospan, decreasing = T)[1:10]]
ENSG00000134184 ENSG00000226278 ENSG00000184674 ENSG00000163682 
      0.7032426       0.6950521       0.6912778       0.6872412 
ENSG00000233927 ENSG00000260246 ENSG00000204792 ENSG00000183298 
      0.6794906       0.6776832       0.6722359       0.6624388 
ENSG00000196436 ENSG00000271581 
      0.6610709       0.6344899 
robospan[order(robospan, decreasing = F)[1:20]]
ENSG00000235795 ENSG00000257307 ENSG00000242100 ENSG00000228205 
     0.01889093      0.01890535      0.01891395      0.01892251 
ENSG00000197830 ENSG00000227344 ENSG00000268543 ENSG00000258782 
     0.01892328      0.01892549      0.01895040      0.01895996 
ENSG00000188505 ENSG00000180389 ENSG00000251791 ENSG00000266501 
     0.01896545      0.01896681      0.01897532      0.01898412 
ENSG00000236992 ENSG00000132698 ENSG00000269038 ENSG00000224415 
     0.01899052      0.01900245      0.01900308      0.01900340 
ENSG00000242571 ENSG00000213590 ENSG00000240254 ENSG00000180211 
     0.01900925      0.01901623      0.01901845      0.01902939 
corrplot(robocov_gtex[,,"ENSG00000242571"],  diag = TRUE,
         col = colorRampPalette(c("lightblue4", "lightblue2", "white", "indianred1", "indianred3"))(200),
         tl.pos = "ld", tl.cex = 0.8, tl.col = "black",
         rect.col = "white",na.label.col = "white",
         method = "color", type = "lower", tl.srt=45)

corrplot(robocov_gtex[,,"ENSG00000134184"],  diag = TRUE,
         col = colorRampPalette(c("lightblue4", "lightblue2", "white", "indianred1", "indianred3"))(200),
         tl.pos = "ld", tl.cex = 0.8, tl.col = "black",
         rect.col = "white",na.label.col = "white",
         method = "color", type = "lower", tl.srt=45)

robospan[order(robospan, decreasing = T)[1:50]]
ENSG00000134184 ENSG00000226278 ENSG00000184674 ENSG00000163682 
      0.7032426       0.6950521       0.6912778       0.6872412 
ENSG00000233927 ENSG00000260246 ENSG00000204792 ENSG00000183298 
      0.6794906       0.6776832       0.6722359       0.6624388 
ENSG00000196436 ENSG00000271581 ENSG00000235231 ENSG00000224114 
      0.6610709       0.6344899       0.6257342       0.6105988 
ENSG00000198502 ENSG00000273295 ENSG00000152726 ENSG00000225760 
      0.6100595       0.6084643       0.5785107       0.5720591 
ENSG00000237039 ENSG00000272004 ENSG00000227827 ENSG00000205571 
      0.5608029       0.5583093       0.5525935       0.5423600 
ENSG00000272955 ENSG00000253570 ENSG00000214425 ENSG00000179344 
      0.5333256       0.5210327       0.5169869       0.5155531 
ENSG00000262500 ENSG00000205578 ENSG00000254353 ENSG00000196656 
      0.5107885       0.5027289       0.5014584       0.4947770 
ENSG00000213058 ENSG00000215513 ENSG00000225972 ENSG00000214110 
      0.4879866       0.4858357       0.4822919       0.4769688 
ENSG00000226210 ENSG00000188234 ENSG00000236682 ENSG00000144115 
      0.4665672       0.4600686       0.4596699       0.4554153 
ENSG00000214401 ENSG00000100376 ENSG00000226752 ENSG00000164308 
      0.4504711       0.4497744       0.4408376       0.4367149 
ENSG00000096060 ENSG00000273018 ENSG00000228078 ENSG00000188933 
      0.4352561       0.4346918       0.4327234       0.4308759 
ENSG00000187010 ENSG00000262539 ENSG00000013573 ENSG00000099984 
      0.4285536       0.4226383       0.4225531       0.4184471 
ENSG00000204525 ENSG00000166435 
      0.4088639       0.3976043 
corrplot(robocov_gtex[,,"ENSG00000179344"],  diag = TRUE,
         col = colorRampPalette(c("lightblue4", "lightblue2", "white", "indianred1", "indianred3"))(200),
         tl.pos = "ld", tl.cex = 0.8, tl.col = "black",
         rect.col = "white",na.label.col = "white",
         method = "color", type = "lower", tl.srt=45)

corrplot(robocov_gtex[,,"ENSG00000214425"],  diag = TRUE,
         col = colorRampPalette(c("lightblue4", "lightblue2", "white", "indianred1", "indianred3"))(200),
         tl.pos = "ld", tl.cex = 0.8, tl.col = "black",
         rect.col = "white",na.label.col = "white",
         method = "color", type = "lower", tl.srt=45)

corrplot(robocov_gtex[,,"ENSG00000011600"],  diag = TRUE,
         col = colorRampPalette(c("lightblue4", "lightblue2", "white", "indianred1", "indianred3"))(200),
         tl.pos = "ld", tl.cex = 0.8, tl.col = "black",
         rect.col = "white",na.label.col = "white",
         method = "color", type = "lower", tl.srt=45)

corrplot(robocov_gtex[,,"ENSG00000015475"],  diag = TRUE,
         col = colorRampPalette(c("lightblue4", "lightblue2", "white", "indianred1", "indianred3"))(200),
         tl.pos = "ld", tl.cex = 0.8, tl.col = "black",
         rect.col = "white",na.label.col = "white",
         method = "color", type = "lower", tl.srt=45)

Session information

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] corrplot_0.84

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1   Rcpp_1.0.1        digest_0.6.19    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.4  
 [7] magrittr_1.5      git2r_0.23.0      evaluate_0.12    
[10] stringi_1.4.3     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.7.0     rmarkdown_1.10    tools_3.5.1      
[16] stringr_1.4.0     yaml_2.2.0        compiler_3.5.1   
[19] htmltools_0.3.6   knitr_1.20

This reproducible R Markdown analysis was created with workflowr 1.1.1