Python Tutorial: Data Visualization with Dokdo API

Community Contributions Tutorials
41

Hi,
I am using "QIIME 2 in a docker" on Linux.
Can I install " [Dokdo API] there as well? Or should I have qiime2 natively and not through docer?

42

Hi @smashha,

I'm not familiar enough with Docker to give you a direct advice, but my understanding is that you can indeed install Python packages after you initialize your Docker image. It's just that any changes to the container will be lost if the container is not committed.

That said, if you want to permanently install Dokdo to your Docker container, then you will probably need to write a Dockerfile that includes the Dokdo installation, which can be found here.

43

Hi,

I am currently use the Qiime 2 through Google colab.
Could you please help me how can I use Dokdo ApI there?

Thanks,
Sara

44

@Sara_Mashhadi_Nejad,

Please see the Installation guide in the link I provided. Let me know if you have any questions afterwards.

45

Hi
Thanks a lot for your help.

I am a beginner in bioinformatics.
To avoid installing other similar software, as I understood from the previous discussion, If we have qiime2 via conda. First, we need to activate our qiime2 and then go and use " git clone https://github.com/sbslee/dokdo cd dokdo
$ pip install ."

Could you please confirm or correct me ?

Thanks a lot,
Sara

46

Sorry, I couldn't wait and tried this way, which I'll describe in steps:

  1. Although I have both qiime2 on Docker and Google Colab, I installed it through " conda" as well.

  2. I activated qiime2 with this command on " qiime2 terminal" : $ conda activate qiime2-amplicon-2023.9

  3. I opened a new terminal and I run the following command there " git clone https://github.com/sbslee/dokdo cd dokdo
    $ pip install . "

  4. In the third terminal I installed " Anaconda Navigator" by the command " conda install anaconda-navigator"

  5. then I tried to open " ANACONDA NAVIGATOR", It brought me to the website and I went through " Anaconda Navigator > Environments > qiime2-amplicon-2023.9 > Open with Jupyter Notebook .

Here are my questions:
Q1. I can see the "qiime2-2023.9" but I do not know, how to open it via, " Jupyter Notebook"?
Q2. How can I use " dokdo" here?

Thanks,
Sara

47

Here is my " conda_list.txt" in my qiime2 environment.
conda_list.txt (51.1 KB)

48

Hi again,

I found my mistakes and tried now it works for me.
I took screenshots of each of the steps that I went through, I will attach them here, maybe it will help some beginners like me.

Thanks a lot,
Sara
How to add dokdo to our qiime2.tsv (1.2 MB)
You can change it to Word or pdf

1 Like
49

Hi again,

This question may seem so basic that I apologize for asking it.
my question is:

All of my "metadata" and all of my "qiime2" results, such as dada2: "denoising-stats.qza", differ from how you used them in Dokdo.
Based on my data, how can I use Dokdo?

Thanks,
Sara

50

code, error, explanation, question:

---Code-------------------------
qza_file = '/home/sara/S1B54/stats-dada2_16S_S1B54.qza'
metadata_file = '/home/sara/S1B54/metadata_sara_R1_Batch1_V3.tsv'

dokdo.denoising_stats_plot(
qza_file,
metadata_file,
'name_abr_source',
figsize=(8, 6)
)

plt.tight_layout()

---Error-------------------------
KeyError: "['merged'] not in index"

---Explanation-----------------------
The columns of my " denosing-stat.qzv" file:

sample-id, input, filtered, percentage of input passed filter, denoised, non-chimeric, percentage of input non-chimeric

---Question-----------------------
As you can see my file does not have these two columns:
merged, percentage of input merged

Please help to resolve the error.
Thanks

51

Hi @Sara_Mashhadi_Nejad, I need to see your input files in order to assess the problem (qza_file and metadata_file). I think it's better to move this conversation to Dokdo's GitHub repository. Could you open an issue there and upload your input files?

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