Heatmap with relative abundances

[beatrizgi...@gmail.com]

Hi, 

I'm trying to do a heatmap with relative abundances instead of using the real OTU counts. Any clue how to do it? 

Thanks, 

Bea. 

[Justine Debelius]

Hi Bea,

There's a QIIME script, normalize_tables.py which you can use to convert your OTU counts to relative abundance. 

You should then be able to make an heatmap using your normalized biom table.

Cheers,

Justine 

[beatrizgi...@gmail.com]

Hi Justine, 

Thanks for the tip. I had a look of the script but I don't really know to convert the OTU counts to relative abundances. I mean, I don't know which argument I might use for it. 

-i, --input_path

Path to the input BIOM file (e.g., the output from OTU picking) or directory containing input BIOM files for batch processing [REQUIRED if not passing -l]

-o, --out_path

Output filename for single file operation, or output directory for batch processing [REQUIRED if not passing -l]

-s, --output_CSS_statistics

Output CSS statistics file. This will be a directory for batch processing, and a filename for single file operation [default: False]

-z, --DESeq_negatives_to_zero

Replace negative numbers produced by the DESeq normalization technique with zeros [default: False]

-a, --algorithm

Normalization algorithm to apply to input BIOM table(s). [default: CSS] Available options are: CSS, DESeq2

-l, --list_algorithms

Show available normalization algorithms and exit [default: False]

Thanks, 
Bea.