Question: Problem with Plotting tool
2
gravatar for mvcarlosdominguez
7 months ago by
mvcarlosdominguez20 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?

ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 7 months ago by mvcarlosdominguez20
0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson25k
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