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Question: Glimma Interactive plots for RNAseq
0
gravatar for Aurora
7 months ago by
Aurora10
Aurora10 wrote:

Hi,

I am using the interactive plots from the glimma package. It works well but I'd like to integrate them in an R markdown document to share it properly. Is is written in Glimma user's guide that  it is possible : "Glimma's interactive plots can be distributed to collaborators by sharing the complete\glimma-plots" folder with its contents. Note that sharing html les alone will not work.
In an Rmarkdown analysis report the interactive plots can be included as links in their
relevant sections"

But I found no way to do it. Does anyone knows how to deal with this ?

Thank you

Have a good day

ADD COMMENTlink modified 7 months ago • written 7 months ago by Aurora10
4
gravatar for James W. MacDonald
7 months ago by
United States
James W. MacDonald48k wrote:

You add links to an rmarkdown file like

[the text goes here](the link goes here)

So if you had your Glimma HTML file in say ./glimma/myplot.html you would do

[here's a sweet plot](./glimma/myplot.html)

ADD COMMENTlink written 7 months ago by James W. MacDonald48k
0
gravatar for Aurora
7 months ago by
Aurora10
Aurora10 wrote:

Ok thank you ! I am gonna give it a try !

But of course if I share my R markdown documents other users won't be able to see the plots as they are stored on my computer

ADD COMMENTlink written 7 months ago by Aurora10
1

If you want to make a comment, please use the ADD COMMENT button.

And you are entirely correct that they won't be able to see links to files that are only on your computer. Which is why you zip everything up, including the plots. Then when they unzip the file, they have everything you had...

ADD REPLYlink written 7 months ago by James W. MacDonald48k

Ty for advices :)

ADD REPLYlink written 7 months ago by Aurora10
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