Can someone show me an example of column annotation file for heatmap?

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Sebastian Lau

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Feb 15, 2016, 2:19:48 AM2/15/16
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Dear all, 

I am very new to gitools. I have an OTU table that I'd like to use gitools to generate heatmap. However, I am a little confused about the format of Column/Row annotation file. I have some annotation for columns as attached. But I don't see gitools can read it. Is there any example/template I can refer to? Many thanks


column-anno-dayu0.01-otu.txt

Michael P Schroeder

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Feb 15, 2016, 3:15:27 AM2/15/16
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Hi Sebastian,

The format seems "almost" fine - it's just that you should transpose the table. This way you will have the Identifiers in the first column and the annotations in the subsequent columns.


See the attached file.

I hope this helps,
Best 



On Mon, Feb 15, 2016 at 8:19 AM Sebastian Lau <yonexh...@gmail.com> wrote:
Dear all, 

I am very new to gitools. I have an OTU table that I'd like to use gitools to generate heatmap. However, I am a little confused about the format of Column/Row annotation file. I have some annotation for columns as attached. But I don't see gitools can read it. Is there any example/template I can refer to? Many thanks


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gitools-annotation-example.txt

Sebastian Lau

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Feb 15, 2016, 5:30:53 AM2/15/16
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Thanks for replying my post Michael!

I generated the annotation file as you showed and gitool seemed to be able to detect the field of my annotation. I use ctrl+click to chose 4 annotation fields and clicked ok to add. However, the heatmap looked unchanged. I didn't see anything new around the column ID. Is this normal or something went wrong? I also noticed the default delimiter was comma.But gitools read tab-delimited input  successfully rather than csv input.

I attached the annotation file I used. Many thanks.

Michael P Schroeder於 2016年2月15日星期一 UTC+8下午4時15分27秒寫道:
otu-anno-tab.txt

Jordi Deu-Pons

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Feb 18, 2016, 6:16:41 AM2/18/16
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Hi Sebastian,

if done a small test with your annotations file and it seems to work.
If you want 4 annotations you have to add 4 headers instead of
selection multiple annotations with ctrl+click. So this is what if
done with the sample data that I'm attaching:

- Right click the columns headers and choose "Add header..."
- Choose "values as text" and click "ok"
- Click "load from file" and select your annotations file
- Then select only de "Obs" annotation and click "next" and then "finish"
- Now you should have a new column header that shows the Obs
annotation at each sample.

I hope this helps,

Best regards


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a10! i fins aviat.
J:-Deu
test.tsv
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