Question: Cytoscape, cannot delete column
gravatar for boczniak767
9 months ago by
boczniak767690 wrote:


I have a problem with deleting columns in one of the networks in Cytoscape file.

Formerly the session file was big, with huge network from which I separated few small. I also used Dynet app to compare the networks and this generated new columns. Then I deleted majority of networks to create smaller file, which I assumed would be smaller on disk and will be loading faster (what wasn't the case but this is unresolved question).

So now I have six networks from which I want to delete some table columns to export whole file to html. For one of the networks there are columns which are un-deletable. It is the case for a subset from other network in which I succeeded in deleting columns. More curiously (and annoying) the unwanted coulmns (reamins from DYnet analysis) shows (and are un-deletable) after recreating the network from original one (which doesn't have this columns).

I thought that I could hide unwanted columns and in html-exported file they doesn't show but it does.

I'd be very grateful for help.

cytoscape • 269 views
ADD COMMENTlink modified 8 months ago • written 9 months ago by boczniak767690

Greetings, You don't what version of Cytoscape you are using, which might be helpful. In any case, if you can send me your network, I can quickly tell you what the problem is. The Cytoscape API does allow you to create immutable columns, but I'm not familiar enough with DyNet to know if they do that or not.

-- scooter

ADD REPLYlink written 9 months ago by scooter330
gravatar for boczniak767
8 months ago by
boczniak767690 wrote:

Ok, so I managed to do what I needed.

Maybe for someone it would be useful.

In short:

  1. I unpacked the cys file and renamed to zip
  2. In tables subdirectory I searched files with instances of "DAP" (the part of a columns' name, which I wanted to delete) and writeit to file grep -rl 'DAP' > x
  3. I used xargs to delete files with 'DAP' hits xargs -I{} rm -r {} < ~/x

The file is still huge (and in the zip there are many not needed remains of deleted networks) but the troublesome colums disappeared.

ADD COMMENTlink written 8 months ago by boczniak767690
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1794 users visited in the last hour