Potential user errors; recommendations for user-centered design.

hms-dbmi / scde

R package for analyzing single-cell RNA-seq data

http://pklab.med.harvard.edu/scde

Other

172 stars 66 forks source link

Potential user errors; recommendations for user-centered design. #5

Open JEFworks opened 9 years ago

JEFworks commented 9 years ago

If column colors are not provided in the app creation (ie. col.cols = NULL), the app still gets created but the heatmaps will not be outputting and throws error:

Error in nrow(results$colcol):1 : argument of length 0

Also in vignette, col.cols is made but never used. Instead we use Pollen's annotations.

JEFworks commented 9 years ago

[x] GO enrichment testing does not work unless user has provided myGOTERM myGOTERM object not easily standardized since users provide the go environment

Update: Addressed in clean.go where annot = TRUE

JEFworks commented 8 years ago

[ ] speed up the R code (a lot) by not calling R_CheckUserInterrupt(); in every single loop iteration but rather only every few thousand iterations. In particular, it’s most efficient to choose a power of 2 for the interval. http://www.r-bloggers.com/performance-calling-r_checkuserinterrupt-every-256-iteration-is-actually-faster-than-ever-1000000-iteration/
[ ] change from depends to imports http://stackoverflow.com/questions/34880161/use-depencies-in-r-packages-through-library-description-file/34883351#34883351