search

adamovanja / qzv-viewer

BSD 3-Clause "New" or "Revised" License
2 stars 0 forks source link

qzv issue #1

Closed FerchoHQ closed 5 days ago

FerchoHQ commented 2 years ago

Hi,

I´m using this tool, I can see all my qzv files too easy, but I have an issue with 3 files:

  1. demux.qzv : I can´t open this file.
  2. barplot: I only see a small figure of qiime2 logo, but not the plot.
  3. rarefactions: I can see the options for metric and sample data column, but I can´t see any option in this part.

Note: I can see normally on https://view.qiime2.org/

Thanks for your time, kind regards. demux_qzv barplot_qzv rarefactions_qzv

adamovanja commented 2 years ago

Hi there,

Thanks for giving this package a try. Yes, as you have found correctly that there are still output visualizations which are not correctly displayed with the qzv-viewer.

However, since you are using Jupyter notebooks, there is another working QIIME 2 notebook extension out there (unrelated to qzv-viewer). You can install it by running the following command in your terminal before opening the Jupyter interface:

jupyter serverextension enable --py qiime2 --sys-prefix

After opening the jupyter notebook with jupyter notebook, you can display all QIIME 2 visualizations inline with the following commands:

from qiime2 import Visualization
Visualization.load(<INSERT_PATH2FILE>)

I hope this helps.

FerchoHQ commented 2 years ago

Hi,

Thank you so much for your help, I'll use this information.

Kind regards.

On Thu, Jun 30, 2022 at 8:48 AM Anja Adamov @.***> wrote:

Hi there,

Thanks for giving this package a try. Yes, as you have found correctly that there are still output visualizations which are not correctly displayed with the qzv-viewer.

However, since you are using Jupyter notebooks, there is another working QIIME 2 notebook extension out there (unrelated to qzv-viewer). You can install it by running the following command in your terminal before opening the Jupyter interface:

jupyter serverextension enable --py qiime2 --sys-prefix

After opening the jupyter notebook with jupyter notebook, you can display all QIIME 2 visualizations inline with the following commands:

from qiime2 import Visualization Visualization.load()

I hope this helps.

— Reply to this email directly, view it on GitHub https://github.com/adamovanja/qzv-viewer/issues/1#issuecomment-1171243254, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMDUXA6NP2NAYLV5QCKB3SDVRWQTTANCNFSM5ZNL5MTQ . You are receiving this because you authored the thread.Message ID: @.***>

adamovanja commented 2 years ago

P.S. for the above command (jupyter serverextension enable --py qiime2 --sys-prefix) to run, you need to install another conda package with conda install jupyter_contrib_nbextensions