frankkramer-lab / mully Goto Github PK

When you remove a layer and set transitive edges to TRUE you often get an error that the edge you are trying to create already exists which stops the whole function from running.

The alternative is

Error in Ops.data.frame(df[j, ], common[i, ]) : ‘==’ only defined for equally-sized data frames

which doesn't seem to be mully based but instead more fundamental

This is more of a feature request or nice-to-have. One thing that really helps (static) 3d images pop is when you add a transparent (but visible) layer, like what you did for the Mully logo or such as in figures 1, 2, 3, and 4 in the manuscript. I can see how in a rotatable 3d image that node size provides depth, but I wonder if it would also be possible to (perhaps optionally) visualize the layer that the nodes are associated with.

If it is easy to mock up, then great, but if not, no worries. I just thought it might be a helpful way for the user to visualize her data.

Seems like only 3 colors are generated at random. This is prohibitive in graphs that have over 3 layers. In addition, it would be great if we could customize the palate (rColorBrewer).

I'm not sure there is an override available to users as the colors are generated inside the plot.mully function. But I am new to R so I could be mistaken.

Hi folks,

I was going through the README.md and when attempting to execute:

print.mully(g12)
I got the following error:

Error in print.mully(g12) : could not find function "print.mully"

However, the print.mully documentation says the usage is:

## S3 method for class 'mully'
print(g)

and when I tried this, it worked, so the README.md should be updated accordingly

Hi folks,

When I attempt to execute

plot.mully(g12, layout="scaled")

I get the following error:

Error in plot.mully(g12, layout = "scaled") : 
  could not find function "plot.mully"

I also noticed there was no documentation for plot.mully when I tried to execute help(plot.mully):

No documentation for ‘plot.mully’ in specified packages and libraries:
you could try ‘??plot.mully’
> ??plot.mully
> 

I am not an R programmer, but I am wondering if the problem is that the NAMESPACE file does not export any of the code in mully_visualization