Enforce code width limit

[Joshua Shapiro]

Background/Problem

Related to #289

Occasionally we have lines of code that get a bit long and don't render well in the html versions of notebooks.
A normal code width limit of ~80-100 characters for a bare notebook is probably too generous at times for html display, especially if users try to narrow their windows.

This seems to occur in our code most often in comments (perhaps because these are not affected by styling), especially when trailing comments occur on a line.

What potential "gotchas" do we know of?

I don't think this is something styler can handle automatically, but if it can, that might be the ideal case. I can't find a line-width argument in its options, though it may be buried somewhere.

formatR was an alternative I looked at that does handle this somewhat, but it seems to not play well with pipes, and is otherwise aggressive.

What are the recommended next steps?

I am compiling a list of wide lines (>70 characters, as tha tis what I used for output in #402) based on the current staging branch, but maintaining this standard in the future will require vigilance, and it should be added to CONTRIBUTING.md at a minimum.

Automated checking would be a nice feature if we can figure out a method.

I am going to add to this issue with separate comments for each file.

Is there a particular timeframe for this issue?

Before going live

[Joshua Shapiro]

• refinebio-examples/02-microarray/clustering_microarray_01_heatmap.Rmd

  Lines 199 to 200 in 9acefe5

     # Here we are going to store the gene IDs as rownames so that we can have a numeric matrix to perform calculations on later 
     tibble::column_to_rownames("Gene") 

• refinebio-examples/02-microarray/clustering_microarray_01_heatmap.Rmd

  Line 233 in 9acefe5

   # Subset the data choosing only genes whose variances are in the upper quartile 

• refinebio-examples/02-microarray/clustering_microarray_01_heatmap.Rmd

  Lines 247 to 249 in 9acefe5

       cluster_rows = TRUE, # We want to cluster the heatmap by rows (genes in this case) 
       cluster_cols = TRUE, # We also want to cluster the heatmap by columns (samples in this case), 
       show_rownames = FALSE, # We don't want to show the rownames because there are too many genes for the labels to be clearly seen 

• refinebio-examples/02-microarray/clustering_microarray_01_heatmap.Rmd

  Line 272 in 9acefe5

     "GSE24862_heatmap_non_annotated.png" # Replace file name with a relevant output plot name 

• refinebio-examples/02-microarray/clustering_microarray_01_heatmap.Rmd

  Lines 294 to 308 in 9acefe5

     # We want to select the variables that we want for annotating the heatmap 
     dplyr::select( 
       refinebio_accession_code, 
       refinebio_cell_line, 
       refinebio_treatment 
     ) %>% 
     # Let's create a variable that specifically distinguishes whether the cell line is parental or resistant -- since this is a key aspect of the experimental design 
     dplyr::mutate( 
       cell_line_type = 
         dplyr::case_when( 
           stringr::str_detect(refinebio_cell_line, "_r") ~ "resistant", 
           TRUE ~ "parental" 
         ) 
     ) %>% 
     # The `pheatmap()` function requires that the row names of our annotation object matches the column names of our dataset object 

• refinebio-examples/02-microarray/clustering_microarray_01_heatmap.Rmd

  Line 348 in 9acefe5

     "GSE24862_heatmap_annotated.png" # Replace file name with a relevant output plot name 

[Joshua Shapiro]

Deleted most comments, because they were way too much here. Plan of attack is to check this as we go through #289 and #290. I will soon file a PR with some changes in 02-microarray/clustering_microarray_01_heatmap.Rmd

I am also thinking that 80 characters is probably a sufficient limit here for most cases, based at least on how things look for me with reasonable window widths most of the time (I like smaller for the output though). I think we should strive to be shorter, but if only comments are getting up toward that limit, we should be fine.