Plot not generated

[In2S]

Hello acvill, I have tried to run bracken_plot, however no plot is being generated.

I am getting this outcome.

Please look into this.

With regrads, In2S

[acvill]

Hi @In2S -- this could be a number of things. I restarted the application and successfully made a plot using one of the example files, so it's not a server issue. If you can try again with one of the example files and it works, then it's likely an issue with your input. The app might hang if the size of the input file requires too many resources to process. Try subsetting your data using the Maximum number of taxa to plot field.

[In2S]

Issue resolved. Thank you for your reply.

On Mon, Aug 21, 2023, 16:31 Albert Vill @.***> wrote:

Hi @In2S https://github.com/In2S -- this could be a number of things. I restarted the application and successfully made a plot using one of the example files https://github.com/acvill/bracken_plot/tree/main/example_data_bracken, so it's not a server issue. If you can try again with one of the example files and it works, then it's likely an issue with your input. The app might hang if the size of the input file requires too many resources to process. Try subsetting your data using the Maximum number of taxa to plot field.

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[In2S]

Hello,

bracken_plot is generating plots in Linux. However, it is running but not generating plots in Windows. Can you help me with this?

With regards, Indu

With regards, In2K/इन2क

Satyanveshi (to seek the truth)/सत्यान्वेषी(सत्य की खोज में)

[image: International Year of Basic Sciences for Development]

On Mon, Aug 21, 2023 at 8:05 PM Albert Vill @.***> wrote:

Closed #4 https://github.com/acvill/bracken_plot/issues/4 as completed.

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[acvill]

Since the app is web-based, there's no simple reason why it wouldn't work on the same browser across operating systems. I'm currently using Chrome v115.0.5790.171 on a Windows 11 machine, and bracken_plot works fine. If you continue running into issues on Windows, you could try downloading the bracken_plot.Rmd notebook and creating plots locally in RStudio.

[In2S]

Ok, thank you for your quick response.

On Tue, Aug 22, 2023, 20:26 Albert Vill @.***> wrote:

Since the app is web-based, there's no simple reason why it wouldn't work on the same browser across operating systems. I'm currently using Chrome v115.0.5790.171 on a Windows 11 machine, and bracken_plot works fine. If you continue running into issues on Windows, you could try downloading the bracken_plot.Rmd notebook https://github.com/acvill/bracken_plot/blob/main/bracken_plot.Rmd and creating plots locally in RStudio.

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[In2S]

Hello Vill,

The maximum number of samples that can be plotted is limited. How can I increase the limit. I am editing App.R file: [image: image.png] But it is not working. IS there something wrong with it? Thank you in advance.

With regards, In2K/इन2क

Satyanveshi (to seek the truth)/सत्यान्वेषी(सत्य की खोज में)

[image: International Year of Basic Sciences for Development]

On Tue, Aug 22, 2023 at 8:29 PM Indu Kumari @.***> wrote:

Ok, thank you for your quick response.

On Tue, Aug 22, 2023, 20:26 Albert Vill @.***> wrote:

Since the app is web-based, there's no simple reason why it wouldn't work on the same browser across operating systems. I'm currently using Chrome v115.0.5790.171 on a Windows 11 machine, and bracken_plot works fine. If you continue running into issues on Windows, you could try downloading the bracken_plot.Rmd notebook https://github.com/acvill/bracken_plot/blob/main/bracken_plot.Rmd and creating plots locally in RStudio.

— Reply to this email directly, view it on GitHub https://github.com/acvill/bracken_plot/issues/4#issuecomment-1688353178, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUV6HUXSZ3JUOCQJUOP32IDXWTCAVANCNFSM6AAAAAA3YEY7EA . You are receiving this because you were mentioned.Message ID: @.***>

[acvill]

Are you using the app.R file to run a local instance of the bracken_plot app in shiny? Instead, if you are trying to recreate the relative abundance plots locally, I would recommend downloading the bracken_plot.Rmd notebook and running the plot_bracken() function with your data in R / RStudio. You can then make adjustments to the ggplot portion of the function to accommodate more samples.

[In2S]

Thank you for your response. It is working fine. How can I cite your Utility in research paper, if there is any paper or link for citation. Please share it.

With regards, In2K/इन2क

Satyanveshi (to seek the truth)/सत्यान्वेषी(सत्य की खोज में)

[image: International Year of Basic Sciences for Development]

On Wed, Aug 23, 2023 at 9:48 AM Albert Vill @.***> wrote:

Are you using the app.R file to run a local instance of the bracken_plot app in shiny? Instead, if you are trying to recreate the relative abundance plots locally, I would recommend downloading the bracken_plot.Rmd notebook https://github.com/acvill/bracken_plot/blob/main/bracken_plot.Rmd and running the plot_bracken() function with your data in R / RStudio. You can then make adjustments to the ggplot portion of the function to accommodate more samples.

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[acvill]

Glad it's working for you. There is no publication associated with the app. You can cite the GitHub repository as follows:

Vill, A. C. (2023). bracken_plot: a Shiny app for taxonomic abundance visualization [Computer software]. https://github.com/acvill/bracken_plot

I would also recommend citing kraken2 and bracken.

https://doi.org/10.1186/s13059-019-1891-0 https://doi.org/10.7717/peerj-cs.104

[In2S]

I have used Kraken2 and Bracken, already cited. Thank you.

With regards, In2K/इन2क

Satyanveshi (to seek the truth)/सत्यान्वेषी(सत्य की खोज में)

[image: International Year of Basic Sciences for Development]

On Wed, Aug 23, 2023 at 9:31 PM Albert Vill @.***> wrote:

Glad it's working for you. There is no publication associated with the app. You can cite the GitHub repository as follows:

Vill AC. bracken_plot: a Shiny app for taxonomic abundance visualization. 2023, GitHub repository: https://github.com/acvill/bracken_plot.

I would also recommend citing kraken2 and bracken.

https://doi.org/10.1186/s13059-019-1891-0 https://doi.org/10.7717/peerj-cs.104

— Reply to this email directly, view it on GitHub https://github.com/acvill/bracken_plot/issues/4#issuecomment-1690226600, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUV6HUT3TE7UDCYO2VZ5DCLXWYSNFANCNFSM6AAAAAA3YEY7EA . You are receiving this because you were mentioned.Message ID: @.***>

[In2S]

Greeting for the day,

I am trying to generate heatmap for beta-diversity obtained from bracken files by following command:

python KrakenTools/DiversityTools/beta_diversity.py -i \ bracken_outputs/SRR14092160.bracken bracken_outputs/SRR14092310.bracken \ bracken_outputs/SRR14143424.bracken --type bracken

However, I am getting this error: Error in heatmap(data) : 'x' must be a numeric matrix

This is the input file: x 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 0 0.000 0.455 0.703 0.600 0.288 0.292 0.571 0.779 0.467 0.737 0.507 0.716 0.558 0.445 0.852 1 x.xxx 0.000 0.637 0.691 0.564 0.345 0.285 0.719 0.661 0.680 0.267 0.517 0.704 0.657 0.821 2 x.xxx x.xxx 0.000 0.769 0.789 0.667 0.530 0.293 0.803 0.248 0.678 0.256 0.757 0.769 0.487 3 x.xxx x.xxx x.xxx 0.000 0.583 0.666 0.696 0.817 0.479 0.790 0.690 0.784 0.381 0.435 0.892 4 x.xxx x.xxx x.xxx x.xxx 0.000 0.436 0.665 0.824 0.409 0.801 0.590 0.775 0.582 0.400 0.885 5 x.xxx x.xxx x.xxx x.xxx x.xxx 0.000 0.484 0.760 0.566 0.714 0.419 0.654 0.636 0.562 0.835 6 x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx 0.000 0.643 0.745 0.603 0.362 0.390 0.719 0.701 0.766 7 x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx 0.000 0.856 0.215 0.726 0.375 0.839 0.823 0.420 8 x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx 0.000 0.834 0.709 0.829 0.449 0.380 0.905 9 x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx 0.000 0.691 0.322 0.796 0.794 0.419 10 x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx 0.000 0.554 0.733 0.680 0.821 11 x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx 0.000 0.800 0.790 0.510 12 x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx 0.000 0.389 0.890 13 x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx 0.000 0.882 14 x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx x.xxx 0.000

With regards,

Indu

With regards, In2K/इन2क

Satyanveshi (to seek the truth)/सत्यान्वेषी(सत्य की खोज में)

[image: International Year of Basic Sciences for Development]

On Wed, Aug 23, 2023 at 9:33 PM Indu Kumari @.***> wrote:

I have used Kraken2 and Bracken, already cited. Thank you.

With regards, In2K/इन2क

Satyanveshi (to seek the truth)/सत्यान्वेषी(सत्य की खोज में)

[image: International Year of Basic Sciences for Development]

On Wed, Aug 23, 2023 at 9:31 PM Albert Vill @.***> wrote:

Glad it's working for you. There is no publication associated with the app. You can cite the GitHub repository as follows:

Vill AC. bracken_plot: a Shiny app for taxonomic abundance visualization. 2023, GitHub repository: https://github.com/acvill/bracken_plot.

I would also recommend citing kraken2 and bracken.

https://doi.org/10.1186/s13059-019-1891-0 https://doi.org/10.7717/peerj-cs.104

— Reply to this email directly, view it on GitHub https://github.com/acvill/bracken_plot/issues/4#issuecomment-1690226600, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUV6HUT3TE7UDCYO2VZ5DCLXWYSNFANCNFSM6AAAAAA3YEY7EA . You are receiving this because you were mentioned.Message ID: @.***>