beta_diversity_through_plots (all variables in mapping file not showing up in pull down menu)

[Alexis Brown]

Hi all,

I ran the following command: beta_diversity_through_plots.py -i otu_table_labcontaminants_removed_filtered_xsectional_normalized.biom -o bdiv_through_plots_jw -t rep_phylo_jw_pipeline.tre -m pigs_mapping_blanks_old_new_alphadivjw_09_27_17_xsectional_corrected_copy.txt

When i opened the html some of the variables are not available within the pull down menu? Can anyoe shed light on why that might be happening?

[Colin Brislawn]

Hello Alexis,

Sorry about the delay in answering this question. My guess is that this is some issue with the mapping file. Maybe the column include characters that qiime does not like. 

If you want to post the first few lines of your mapping file, we can see if we can figure out why some of the columns don't work. You could also validate your mapping file to check for issues:

http://qiime.org/scripts/validate_mapping_file.html 

Colin

[Nancy Moreno]

Hi Alexis, 

I had a similar issue. I was missing the column that contained PD whole tree alpha diversity measures.

After reducing my PD whole tree alpha diversity measures to 3 decimal places and rerunning a core diversity analysis with this modification to my mapping file, the column showed up.

For some odd reason emperor doesn't like many decimal places.

Hope this helps,

Nancy

[Colin Brislawn]

Hello Nancy, Alexis,

I should have mentioned this before: emperor will drop columns in which every value is unique, unless you pass the --add_unique_columns flag when running the script. I bet reducing your decimal places make some of the values the same, and thus the script included this column.

Let me know if this helps,

Colin