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Heatmap with prettified names? #24
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Thanks for the great suggestion! I just added the
Is this what you had in your mind? Let me know if you need more help. |
This is wonderful - thanks for your prompt response. Based on your figures, this is just what I was looking for. I'll give it a whirl today. |
OK @sbslee ,I've been able to implement that new function - thank you! Now I'm wondering...
Michelle |
Thanks for the great ideas. I think I can implement both fairly easily, but let's take one step at a time. I just added the
If you are happy with above, we can move on to the next (i.e. showing top taxa). Let me know what you think. |
Works exactly as I was hoping - thanks @sbslee! |
Glad to hear that works for you. As for the rotation of tick labels, AFAIK, it is automatically determined by the
It sounds like we are good to move on to the next task: showing only the top taxa. Stay tuned. |
@sbslee I have just realised the 'prettified names" function actually truncates species names to just show the s__name, not g__Genus; s__species name. I just noticed this in the Is there a way to return the last two ranks - so in your example,
I am using taxonomy from NCBI that separates the genus names and species names - so with the 'prettified names', it is impossible to tell which genus the species come from. (BTW, I can make this a separate issue if that is better). |
No worries about opening another issue. And thanks for the great suggestion. I myself have come across that issue before. The good news is I just updated the
Will produce the usual:
However, if you provide the
It will give what you want:
I extended this to the
Updated documentations: pname: https://dokdo.readthedocs.io/en/1.11.0-dev/dokdo_api.html#module-dokdo.api.pname Does this work for you? |
That looks great to me @sbslee - I hope yourself and others will find it useful as well. I really appreciate you making these adjustments and answering my questions. |
No problem! I also added the
Let me know if this is what you wanted. |
Fantastic @sbslee! This has worked perfectly with my data. Thank you again for adding those options to your code. I'm so grateful that I found Dokdo and that you are still actively working on it. |
Hi @sbslee ,
Thanks for your very recent updates to heatmap (from clustermap) - just in time for what I need. Just wondering how I could incorporate your 'prettified names' function - to get taxa names as the y-axis labels such as is possible in the legend of the taxa_abundance_bar_plot output?
Thanks,
Michelle
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