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.
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.
Keep us posted!
thermokarst
(Matthew Ryan Dillon)
unassigned thermokarst
#4
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.
thermokarst
(Matthew Ryan Dillon)
assigned thermokarst
#8
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!
thermokarst
(Matthew Ryan Dillon)
unassigned thermokarst
#10