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Add alpha diversity data to a mapping file for use with other QIIME scripts, i. e. make_emperor. The resulting mapping file will contain three new columns per metric in the alpha diversity data; the first column being the raw value, the second being a normalized raw value and the third one a label classifying the bin where this value fits based on the normalized value.
Usage: add_alpha_to_mapping_file.py [options]
The result of running this script is a metadata mapping file that will include 3 new columns per alpha diversity metric included in the alpha diversity file. For example, with an alpha diversity file with only PD_whole_tree, the new columns will PD_whole_tree_alpha, PD_whole_tree_normalized and PD_whole_tree_bin.
Adding alpha diversity data:
Add the alpha diversity values to a mapping file and classify the normalized values into 4 bins, where the limits will be 0 < x <= 0.25 for the first bin 0.25 < x <= 0.5 for the second bin, 0.5 < x <= 0.75 for the third bin and 0.75 < x <= 1 for the fourth bin.
add_alpha_to_mapping_file.py -i adiv_pd.txt -m mapping.txt -b 4 -o alpha_mapping.txt
Adding alpha diversity data with the quantile method:
Add the alpha diversity values to a mapping file and classify the normalized values using the quartiles of the distribution of this values.
add_alpha_to_mapping_file.py -i adiv_pd.txt -m mapping.txt -b 4 -o alpha_mapping_quantile.txt --binning_method=quantile
Adding collated alpha diversity data:
Add the mean of the alpha diversity values at a specified rarefaction depth, this case is for use with the output of collate_alpha.py. It is recommended that the filenames are the name of the metric used in each file.
add_alpha_to_mapping_file.py -i 'shannon.txt,chao1.txt' -m mapping.txt -b 4 -o collated_alpha_mapping.txt --depth=49 --collated_input