debsin/dropclust

Version 2.1.0 released

dropclust's Issues

This does not install as an R package

This is a great comprehensive repository of supplementary material for your publication. However, it is not an "R package" as the publication states. This is much more difficult to install (with hardcoded directories) than a typical R package. At the moment, it is difficult to tell what the package does, let alone install or run it.

I would suggest to format (and document) this tool as an R package using devtools and roxygen2. Dependancies can be listed in the DESCRIPTION file and will be installed with your package. Python and C++ codes can be called with the reticulate and Rcpp packages respectively. This would make it much more convenient for users to install and run the code. This way more people will use your tools and cite them. Please refer to this guide for how to develop R packages: http://r-pkgs.had.co.nz/

error in Sampling(sce,optm_parameters=TRUE)

Hello
when I use the packsge dropClust, the number of cells in ecpression matrix > 500,run Sampling(sce,optm_parameters=TRUE),
the error is:

• 'list' object cannot be coerced to type 'double'

  I download the source code ,and find where the error from:
  

• sampling part :output <- as.numeric(partition)

Please check to see if it is correct,And tell me how to fix it
Thank you!

Error in Tutorial

While doing the tutorial when I run this code 'ScatterPlot (plot_data, title = "Clusters")', I got the following error.

Error in (function (classes, fdef, mtable):
'unable to find an inherited method for function' reducedDims 'for signature ‘" data.frame ""'.

What should I do?

louvain_script.sh missing

Hello,

I can't find louvain_script.sh anywhere -- would you please be able to add it?

The error is:

sh: louvain_script.sh: No such file or directory

Thanks!