I want to create a heatmap for my analysis, but I have an error for it. First I filter my table based on this page: https://docs.qiime2.org/2017.11/plugins/available/feature-table/filter-features/
then I filter my table based on the frequency only to obtain desired visualized taxa in my heatmap and I get artifact file as attached below. After that, I try to generate heatmap using this command:
qiime feature-table heatmap
--i-table filter-table-heatmap.qza
--m-sample-metadata-file metadata1.tsv
--m-feature-metadata-file metadata1.tsv
--p-metric braycurtis
--o-visualization heatmap.qzv
then I got the following error message: (1/2) Missing option "--m-sample-metadata-column". (2/2) Missing option "--m-feature-metadata-column".
After I got those message, I retried using this command:
qiime feature-table heatmap
--i-table filter-table-heatmap.qza
--m-sample-metadata-file metadata1.tsv
--m-sample-metadata-column source
--m-feature-metadata-file metadata1.tsv
--m-feature-metadata-column source
--p-metric braycurtis
--o-visualization heatmap.qzv
then I still got the error message as follows: Plugin error from feature-table: Cannot visualize an empty table. Debug info has been saved to /tmp/qiime2-q2cli-err-ogp2kysh.log
Please help me to solve that problem. Did I wrong with my command? or I have some mistakes with my metadata file or filtered table? I also attached my metadata file for further consideration.
Thank you for your kind response.
Step 2: verify that table is empty (feature-table summarize):
Step 3: check provenance to see what kind of filtering was done
Apparently you filtered in 4 separate steps. I would go back and double check which step is producing the empty table, then we can chat more about why its creating an empty table.
Honestly I got this table after 4 times of filtering step (I'm beginner using QIIME2 and I just learnt it by my self from some forum topics). I did that because I want to eliminate some taxa from my table according to taxonomic assignment, so I decided to filter it using p-exclude. There were 3 taxa I would exclude for my downstream analysis, so I did it one by one until I got a table before filter it based on frequency (and filter-table-heatmap.qza artifact was a final one after filtering by its frequency) . Does it a problem for my final table artifact?
Dear @thermokarst, after I recheck my previous table (which I used for filter-feature step as an input), it had a value inside it (not an empty table).filter-table-fix.qza (58.6 KB) filter-table-fix.qzv (445.9 KB)
After that I directed to filter-feature step using those table using following command: qiime feature-table filter-features --i-table filter-table-fix.qza --p-min-frequency 100 --p-max-samples 20 --m-metadata-file metadata1.tsv --o-filtered-table filter-table-heatmap.qza
then I check it using feature-table summarize and got the same result as you did filter-table-heatmap.qzv (405.1 KB) . Is there some mistakes with my parameter during filter-feature?
Thank you for your help.
Here you appear to be providing Sample metadata when filtering Features - the sample IDs will not match any of your feature IDs, which is why the table is filtering to nothing. Drop that line and try again!
. Does it a problem for my final table artifact?