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how to make heatmap with text file #22
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@khemlalnirmalkar, thanks for the question. First of all, I just updated the
Example CSV file for creating input Next, if you want to group the samples but do not want to cluster them, you can set
I understand these are not exactly what you wanted, but I hope this is a good starting point. What do you think? |
@sbslee , |
If it's something that's not too difficult to implement, I'd be more than happy to make updates do Dokdo. So please keep letting me know :) That being said, I updated the
Next up is splitting a heatmap by the sample group. This one is trickier because each sample group will have a different clustering pattern because their microbiome composition will be different. In the example you provided, there are only 30 taxa labeled, which indicates to me that the clustering was performed earlier and you are just using the same order of those 30 taxa (I'm not sure how you got the exact order) for all four sample groups. Can you give me a link to the method's documentation so I can read about it? Or explain to me how you generated the example? |
Hi @sbslee |
Good news! Once I realized that some users like yourself don't need (or want) clustering of their samples and/or taxa, I decided to rename the Below is a simple example:
We can display a heatmap for each sample group:
Let me know what you think. I will probably make some additional updates to this method before releasing the official |
@sbslee, Khem |
Those are great questions. I updated the
P.S. AFAIK, microbiome relative abundance data will give best results when normalized with log-based transformation such as log10 and CLR. This is because those data often contain lots of zeros and also extremely large values; therefore, the Z score transformation, which is linear and not log, may not be suitable for this kind of data. Please use this option carefully. |
@sbslee Thanks for the quick action. |
@sbslee, Dokdo needs "s__" for taxa, but is it possible to avoid it? i am thinking to use for metabolites too. Thanks, |
Hope this helps. Let me know if you need more help. |
I thought about this more, and I think the following might help in your case. Basically, I added the
Let me know what you think. |
@sbslee Awesome, Thanks again, |
No worries, you are more than welcome to ask as many questions as you want! Generally speaking, the
That being said, I'm getting the impression that you want to adjust the coloring scale just for selected species (e.g. Prevotella species), and if that's the case, then it's not possible with the You could selectively perform some sort of scaling in your input I think the best bet is drawing another heatmap for Prevotella species, as you mentioned, but I personally find your plot above perfectly acceptable, so I wouldn't even bother drawing another plot. But that's just my take! Feel free to ask any follow-up questions. |
@sbslee earlier, I did try with vmin and vmix but was not helpful, |
Sounds good. One thing to note is that if you are going to plot a separate figure just for Prevotella species, you may have to create a |
@sbslee Agreed..yes, the plan is use panda.dataframe only for Prevotella sps. Thanks for the suggestion :) |
Hi @sbslee ,
Is it possible to make a heatmap using a panda dataframe (not qza)?
i am trying to replicate the same style like bar plot, splitted categories with and without dendrogram.
Please can you help?
like this image
Thanks,
Khem
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