PCoA graphical future?

User Questions
1

Hello!

Are there any plans to introduce more refined PCoA graphical controls? Such as setting exact axes ranges, grouping oval thickness, etc.?

Cheers,
Pauleon

2

Let me know which aspects of the visualization you would like to control and I will look into this…

3

As the cluster analysis window currently exists, it scales dynamically with the size of the window and can be “zoomed to fit”. Which is great, but if two PCoA’s are placed side by side with different inputs they may seem as though they have the same cluster separation when in reality they have differing axes dimensions. A few aspects that would be great to control:

-Setting PC axes ranges
-Setting PC unit increments (e.g. controlling whether the axes mark increments of 0.1 or 0.5 PC units)
-Setting the color and thickness of PCoA axes (preferably through an option in the edit menu, or right clicking the axes, or maybe a tab in the format window.)
-Altering the thickness and color of the ellipses formed when you create groups (it seems I’m able to control the thickness of the lines that directly connect the groups by selecting them, but not the ellipses, the color of the ellipses seems at the mercy of the sample colors)

Thanks for the response,
Pauleon

4

Dear Pauleon,

I have implemented all the color and line-width controlling features (there will a list of options in the edit menu for this).
I will look into controlling the PC axes later in the week, when I find time…

5

Please see version 6.15.0
It allows you to set the colors and line widths for the axes, biplot and triplot arrows, and group ellipses and convex hull.
I have also added a feature to set the scaling factor used for the plot. I hope that this will allow you to compare different plots on related data. (Programmatically zooming to a specific setting of the axes is quite difficult to implement…)

6

Thank you Daniel,

I will put these changes to use!

-Pauleon

7

Is there also some option to control the length of the biplot arrows?
I could not find one, but it would be appreciated.
Best regards

8

I have just added two menu items for this under PCoA->More.
This will be available in the next release.

9

Thank you @Daniel ! It would be great, if this can also be configured via the command line / command input.
Best regards, Bernhard

10

If you are running MEGAN UE, then you can use the command

set biPlotScaleFactor=3.0;

to set the scale factor for the BiPlot to 3, say.

MEGAN will “remember” any changes to the biPlotScaleFactor and triPlotScaleFactor, so you won’t have to keep settings these values.

These values are stored in the preferences file Megan.def, so another way to set these values is to edit that file and to add/change a line like this:

BiPlotScaleFactor=3.0