I want to obtain a taxa barplot using relative abundance data. I see that Taxa barplot plugin uses a FeatureTable[Frequency], but I wonder if it could use a FeatureTable[relative frequency] instead.
The problem with FeatureTable[Frequency] is that it does not normalize taxa abundance by the total number or reads of each sample. For instance:
S. aureus sample 1= 1000; Sample 2= 100; Sample 3= 2000; Sample 4= 160
E. coli sample 1= 100; Sample 2= 10; Sample 3= 500; Sample 4= 500
If I group samples 1 and 2 as ‘healthy’ and samples 3 and 4 as ‘sick’, when I perform taxa barplot over those two groups, differences in samples 1 and 3 will have more importance that 2 and 4, because samples 1 and 3 have more total number of reads, since it performed the mean using the sum of the number of reads of each taxa in each sample / number of samples inside the group, instead of using the mean of the relative frequency of each taxa in each sample.
I followed these steps:
qiime feature-table group --i-table UPSTREAM/filter-finished-data/table-only-bacteria-rarefied.qza --p-axis sample --m-metadata-file metadata.tsv --m-metadata-column "Group" --p-mode mean-ceiling --o-grouped-table UPSTREAM/Group-grouped-table.qza qiime taxa barplot --i-table UPSTREAM/Group-grouped-table.qza --i-taxonomy UPSTREAM/taxonomy/taxonomy-silva.qza --m-metadata-file metadata.tsv --o-visualization diversity/beta-div-taxa-bars/taxa-bar-plots-Group.qzv qiime tools view diversity/beta-div-taxa-bars/taxa-bar-plots-Group.qzv
Sorry if I did not explain myself properly. Thanks!