Plot of isomiRs/miRNA distribution using ggplot-python

[lpantano]

Implement option in stats sub-command like --detail to:

[ ] show distribution of sequences per sample (geom_density) [ ] boxplot distribution per sample after normalization like DESeq2 [ ] summary figure like isoPlot(type = "all") from isomiRs bioc package

[cranewen]

Hi Lorena,

I have been working on the plot. I couldn't make the plot correctly in ggplot. It seems missing y axis values. But it works for dots or lines graphs. It looks like that. Please let me know if you have any idea on that.

Or I can make it with Plotly, it looks like this:

What do you think?

[lpantano]

Hi,

That seems a good format as well. But I see all of them looks like 1, is that a typo? If we the right numbers as it is in the example code, you can make a PR to the code adding the code inside the mirtop/plot folder.

Thanks a lot!

On Jan 20, 2018, at 12:42 PM, cranewen notifications@github.com wrote:

Hi Lorena,

I have been working on the plot. I couldn't make the plot correctly in ggplot. It seems missing y axis values. But it works for dots or lines graphs. It looks like that. Please let me know if you have any idea on that. https://user-images.githubusercontent.com/9448300/35186254-33e64cb4-fddf-11e7-81da-c52bf911b15b.png Or I can make it with Plotly, it looks like this: https://user-images.githubusercontent.com/9448300/35186219-aa0c5a60-fdde-11e7-8ef3-f1c399a58e72.png What do you think?

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[cranewen]

Hi Lorena,

No, it's not a typo. It's the problem I am facing now. If I use line or point plot, it shows below, which is what I expected. The code is ggplot(df, aes(x='tool',y='counts')) + geom_line() + facet_wrap('category')

But in the bar chart, ggplot(df, aes(x='tool',y='counts')) + geom_bar() + facet_wrap('category') I don't think y='counts' works in the function.

I will pull request once I fixed this problem. If you know what's wrong here, please let me know.

Thanks, Crane

[lpantano]

Thanks for working on this.

Can you try to add this option inside geom_bar function: stat = “identity",

And see if that fixes the issue.

Cheers

On Jan 23, 2018, at 8:57 AM, Crane Wen notifications@github.com wrote:

Hi Lorena,

No, it's not a typo. It's the problem I am facing now. If I use line or point plot, it shows below, which is what I expected. The code is ggplot(df, aes(x='tool',y='counts')) + geom_line() + facet_wrap('category') https://user-images.githubusercontent.com/9448300/35278883-622fac6e-0019-11e8-82d9-66534758088e.png But in the bar chart, ggplot(df, aes(x='tool',y='counts')) + geom_bar() + facet_wrap('category') I don't think y='counts' works in the function.

I will pull request once I fixed this problem. If you know what's wrong here, please let me know.

Thanks, Crane

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[cranewen]

No, it's the same.

[lpantano]

Other option is to plot a point instead with geom_point and increase the size a little. We can try to figure out the issue later as well.

Thanks!

On Jan 23, 2018, at 9:24 AM, Crane Wen notifications@github.com wrote:

No, it's the same.

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[cranewen]

Sure, Lorena. But I will try to find out a way to plot it in bar charts tonight. Do you want me to pull request? I also did column 9 of GFF and return key #25. I am gonna keep working on all the issues. I now have time during the nights, and I am learning the whole project slowly:)

[lpantano]

Yes, please, one pull request per issue. And please, update the REAMDE.md with your name in the contributors section.

Thanks