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Question: Problem with Plotting tool
2
gravatar for mvcarlosdominguez
11 months ago by
mvcarlosdominguez • 20
mvcarlosdominguez • 20 wrote:

I need to make a rarefaction curve and i´m want to to this:

Plotting tool  with the following parameters “Plot Title” to
Rarefaction “Label for x axis” to Number of Sequences “Label for y
axis” to Number of OTUs “Output File Type” to PNG Click on Insert
Series, “Dataset” to the collapsed rarefaction curve collection Set
Header in first line? to Yes “Column for x axis” to Column 1 “Column
for y-axis” to Column 2 and Column 5 and every third column until the
end (we are skipping the low confidence and high confidence interval
columns)

THE THING IS THAT "PLOTTING TOOL DOESN´T ALLOW ME TO SELECT THE "Dataset" to the collapsed rarefaction curve collection. ALSO I CANT FOUND THE OPTION TO SELECT MY "Output file type"

SOMEBODY CAN HELP ME?
metagenomics gtn help tuturial plotting tool • 354 views
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modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 11 months ago by mvcarlosdominguez • 20
0
gravatar for Jennifer Hillman Jackson
11 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you are working at Galaxy Main (https://usegalaxy.org), the Plotting Tool is pending an update to be compatible with the functions mentioned in the GTN's metagenomics tutorial. Full details and progress on the update can be reviewed here: https://github.com/galaxyproject/usegalaxy-playbook/issues/71

The tool is already upgraded both in the Tool Shed (for use in a local/docker/cloud Galaxy) and at the Freiburg Public Galaxy server here: https://galaxy.uni-freiburg.de. I haven't run through the entire tutorial at the Freiburg server since the latest Galaxy release 17.09, but please ask questions if you run into anything else confusing in the tutorial or that you simply would like more help with - wherever you decide to work.

For the input selection, this is a dataset collection. This means that once you open the "Series" sections for the tool, hover over the icons for the input Dataset and click on the far right icon labeled "Dataset Collection" and you'll find the collapsed rarefaction dataset listed. You'll be opening multiple Series sections, choosing column1 as the X-axis and column2 for the Y-axis. Then opening another Series section and choosing column1 as the X-axis and column5 for the Y-axis. Repeat this for every 3rd column for the Y-axis section to produce the same graph as in the tutorial. I agree that this step could be made a bit more clear in the tutorial instructions and am following up on that.

GTN Tutorial for reference: http://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 11 months ago • written 11 months ago by Jennifer Hillman Jackson ♦ 25k
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