Error in vignettes/tutorial.Rmd

[hyunhwan-jeong]

Regarding a1fd3f1e5bb816488383e6b902b201e3a1d0ae91, I failed to run circular_histogram(mutations,ref) which is at the end of the tutorial. Here is the error message:

Error: xleft, ybottom, xright, ytop should have same length.

The following message is the traceback.

4.
stop(x, call. = FALSE) 
3.
stop_wrap("xleft, ybottom, xright, ytop should have same length.") 
2.
circos.rect(df$start[i] - 0.4, df$y[i] - df$count[i] + 1, df$start[i] + 
    0.4, df$y[i], col = colors[df$mutate_to[i]], border = NA, 
    track.index = 1) at circular.R#97
1.
circular_histogram(mutations, ref) 
-- | --

What I figured out is there is an error during executing circos.rect (Line #97 in R/circular.R).

[JasperYH]

Now it should be fine

[hyunhwan-jeong]

@JasperYH

I have reverted your latest update of vignettes/tutorial.Rmd to my previous version. Please review b5d76e4 and I put some comments on why I have reverted.

• Sourcing R files is also prohibited by CRAN. Please import using library(traceQC) after you build the package instead of Do not source your R files. You can build it by pushing cmd+shift+B or Build -> Install and Restart. library(traceQC) will do import all functions from files which are in R folder.

• Regarding accessing files in inst/extdata/test_data, I suggest accessing files using system.file. After you have installed a package only way to locate the files in inst is that using the function. In other words, you need to declare system.file("inst", "dir2", ..., "file", package="the_package_name") to access the files.

• And ref <- "./test_data/ref.txt" which is the first line of circular_histogram, shouldn't be there, right? I still have some issues with the function, we can discuss about it tomorrow if you want.