trajectory plots unidentifiable.

[yeroslaviz]

Hallo again. I'm honestly impressed by the modifications and fixes you're doing to the program. Thanks a lot for that.

I would like to better understand the trajectory and trajectory_trends plots I can now create from the command line.

1. Running wot trajectory withe the --embeddingoptions creates one png file woth the plot. The file name though get this tilte traj_1.0.4_None_trajectory.png. What is the meaning of None?
   This says even when using specific cell_sets.

2. Running wot trajectory_trends with --plot create also png file(s). Also these files are somehow not defined. The file name get this format
   'trends_1.0.4_Unnamed: 2.mean.txt' and 'trends_1.0.4_Unnamed: 2.png'.
   2.1 It would be great if no spaces or symbols are added to the names, so that it would be easier to handle.
   2.2 What is the meaning of Unnamed?
   2.3 When I use the --gene_filter option (in my example i took only two genes) i get one plot, but when not using this option I get multiple files

'trends_1.0.4_Unnamed: 1.mean.txt'
'trends_1.0.4_Unnamed: 1.png'
'trends_1.0.4_Unnamed: 2.mean.txt'
...
'trends_1.0.4_Unnamed: 5.png'
'trends_1.0.4_Unnamed: 6.mean.txt'
'trends_1.0.4_Unnamed: 6.png'
'trends_1.0.4_Unnamed: 7.mean.txt'
'trends_1.0.4_Unnamed: 7.png'

I have stopped the command than, as I can't see the differences. Can you explain this?

thanks again for all the help

[joshua-gould]

Please see the examples of running trajectory and trajectory_trends at https://github.com/broadinstitute/wot/blob/master/notebooks/command_line_example.sh. For the trajectory tool with the embedding flag, you will get png of the form
wot_trajectory.png. The trajectory_trends command produces 2 files per trajectory: trends.png and trends_.mean.txt.

[yeroslaviz]

But this is not exactly the names I get. Do the additional "None" in the first and "Unnamed" in the second plot have a meaning?
why do I get multiple trajectory_trend plots?