Questions regarding command line

User Questions
1

Hello,
I have 2 questions when I am running the MEGAN6_UE in command line.

  1. In the main windows of taxonomic classification, when I want to export the image, the font in the left or right hand size is invisible, and it seems in exceed the image edge. Even when I try to set up the window size (e.g., set windowSize=3154 x 6085;
    ) or contract the image (contract direction=horizontal;), it does not help. How can I make all the information visualized?
  2. In the same main windows of taxonomic, I wish to make a pie chart or bar chart, and then I showed the pie chart windows and export the image, I can only get the image of the main windows instead of the pie chart. Do you have any solution that I can export the pie chart?
    Thanks for the assistance and clues.

All the best,
Ming

2

Dear @Ming,

Apologies for the delayed response. Could you please share the command you are using?

Best regards,
Anupam

3

Hello, Anupam,

Thanks for the response. Below is one of the scripts:
open file=‘/data/Jiaming.Zhou/SRR8305972_unicycler.rma’;
open viewer=Taxonomy;
update;
set windowSize=3154 x 6085;
collapse rank=‘Genus’;select rank=‘Genus’;
zoom what=full;
show chart drawer=BarChart data=‘Taxonomy’;
contract direction=horizontal;
exportImage file=‘/data/Jiaming.Zhou/taxonomic_viewer.svg’ format=svg visibleOnly=false textAsShapes=true title=none replace=true;
quit;

In this case, I expect to export the image of the barchart. However it export the taxonomic image. I would be very thankful for your clues and suggestion.

Best,
Jiaming

1 Like
4

Dear @Ming,

You need to add set context=TaxaChart;, after show chart drawer=BarChart data=‘Taxonomy’; .

open file=‘/data/Jiaming.Zhou/SRR8305972_unicycler.rma’;
open viewer=Taxonomy;
update;
set windowSize=3154 x 6085;
collapse rank=‘Genus’;select rank=‘Genus’;
zoom what=full;
show chart drawer=BarChart data=‘Taxonomy’;
set context=TaxaChart;
contract direction=horizontal;
exportImage file=‘/data/Jiaming.Zhou/taxonomic_viewer.svg’ format=svg visibleOnly=false textAsShapes=true title=none replace=true;
quit;

let me know if have further questions

Best,
Anupam