tutorial of heatmapmaker

[carolynzy]

I'm using HeatMapMaker with GEO-SPHERE package, beast version 2.5.1 and GEO_SPHERE version 1.2.0. I couldn't find instructions for these parameters in HeatMapMaker: Jitter, Repeat, Mask, clade, and Root only. Do I missed something in the tutorial? It seems the software has been updated but the tutorial is not. I want to change the color range for the dots, which represents their age. How should I do that? Many thanks for this wonderful tool! I really enjoyed using it very much.

[rbouckaert]

@carolynzy to find out what these items mean, you can hover over the field in the HeatMapMaker GUI, or from a terminal call applauncher HeatMapMaker -help, which shows (among other entries):

• jitter jitter applied to dot locations (in pixels)
• mask image file with a mask: dots will not be shown outside mask
• repeats number of times a dot should be drawn
• rootOnly [true|false] only draw root locations and ignore the rest
• clade Name of XML file containing a single TaxonSet in BEAST XML format. If specified, the location of the MRCA of a clade is used (and the rootonly flag is ignored).

Let me know if any of this is unclear.

There is no way to change the colour range other than to change the code at the moment -- will look into this.

[rbouckaert]

Since this is an issue for the GEO_SPHERE package, I opened an issue with that package here: https://github.com/BEAST2-Dev/beast-geo/issues/7

[rbouckaert]

A feature was added to the HeatMapMaker to allow setting the start colour and range of colours, available in GEO_SPHERE v1.2.1.

The tutorial is now updated, available here: https://github.com/BEAST2-Dev/beast-geo/releases/download/v1.2.0/phylogeography_s.pdf

Hope this fixes the issues you were running into. Let me know if you run into any further problems.

[826187573]

Dear Sir, I'm using HeatMapMaker with GEO-SPHERE package, beast version 2.5.2 and GEO_SPHERE version 1.2.0. I input the Tree Set and Background, but it always wrong. It shows in attached. Could you please sent me what you set in "HeartMapMaker Editor", your Tree Set and Background. I want to recurrent the Heart Map in the tutorial. Thank you very much.

Best wish

[rbouckaert]

There was an issue with HeartMapMaker that was fixed in a version later than 1.2.0. Can you upgrade GEO_SPHERE and let me know if the problem persists? Upgrading is easiest via BEAUti using the menu File/Manage packages, then select GEO-SPHERE in the list and click the "Install/upgrade" button.

[826187573]

Thank you, Sir, I upgrade to the lasted version 1.2.2, but the problem persists. I'm not sure if the problem is on my settings of "HeartMapMaker Editor". Maybe the file of Tree Set and Background?

[rbouckaert]

Thanks for the feedback -- can you try to run with minimal changes of the input value: start with only the tree file, then (if that succeeds) add background image and other parameters. Please let me know whether the error persists.

[826187573]

I just input the tree file, succeed. But when background image added, it shows the same error. It is my background image.

[rbouckaert]

When I follow the link to the image, my browser (Firefox) says the image cannot be displayed because it contains errors. I suppose that is the source of the problem. Perhaps the image needs to be converted, e.g., using Image Magic, Gimp or photoshop.

[826187573]

Yes, I tried another image, and it shows as follow. I don't know what the background image needs to be asked. It can output a png file, but the same as the background image.

Loading background image C:\Users\Administrator\Desktop_20190514220417.png No mask image translation map size = 3 Parsing trees D:\master\beastﾳﾢￊￔ\geo+BDSKYseril\2mcc.tree ... done Drawing dots... |=========|=========|=========|=========|=========|=========|=========|=========|=========|=========| done Writing file heatmap.png done Writing legend null\legend.png done in 1 seconds All done

[rbouckaert]

There are a number of possible reasons for this:

• the tree file does not contain geographical data. If so, the image produced without using a background should be blank.
• an incorrect name for the metadata tag is used (tag input in the dialog), which should also give a blank image when no background image is used.
• if the image without background image is not blank, perhaps you should use more replicates (increase repeats) or disc size (discSize entry in the dialog) or decrease translucency (by increasing translucency). Hope this helps, Remco

[826187573]

Thank you so much! I have got a perfect heatmap.