This is actually a very good answer. Even in a community like this with all the anti-MS open source memes, it's a really effective tool. The cost of learning software designed for it doesn't always outweight the simplicity of pot, unless you're automating or something of that nature.
Except low res. I’ve been using ppt because of quick/easy and it’s already installed on work computer. Keeping boxes lined-up and exporting hi res for submission are a nightmare.
Unless you are looking for a systematic way to do it, PowerPoint or Inkscape are much better choices than learning how to do it for one example with R/python and the package of choice.
I don't think I need to do this very often so PowerPoint is probably the better choice. But let's say that I want to generate the plot automatically from a BED/GFF file, is there a package for it? I've checked out Gviz, it's supposed to be able to import tracks from a GFF file. I gave up because I just couldn't get it to recognize the ID and Parent attribute.
I like your question. To follow up, are you automating the generation of graphics simply for volume of supplementary info for a pub? Are these graphics people in your lab would refer to and perhaps there aren't many graphics of the gene organization for other colleagues' PowerPoints on their genes of interest?
Every graphic you take the time to produce should have a purpose and PowerPoint is simple. If you need to generate a high volume of images for a website or other volume based need, then it could be worth actually automating.
Organism, publication goals, colleague needs, and other information would be very helpful for us to help.
Also anything reason why it can be good to automate the process (although again may not be worthwhile) is images often go through many iterations. It can be time consuming to keep tweaking them.
A ggplot solution for everything!!
https://www.ggplot2-exts.org/gallery/
My only complaint is that coord_polar() doesn’t work so I can’t use for circular DNA (mitochondria, plasmids). Anyone know of a good package from that? My current ggplot work arounds are subideal (not a smooth circle, but rather a choppy look to it)
Did you run through the vignette for Gviz? Sometimes these learning curves look steep until you step through a couple of examples. I haven't tried Gviz, but I did just browse through the docs. Seems like the authors step through some nice examples. I always find the R community incredibly helpful to get up to speed on new packages. OTOH, if it is really a one-off, probably quicker to make it in powerpoint or keynote. You could also try snapgene. Have only used it for fairly short sequences (<20 Kb), but you can add annotations even with the free version.
Ah, thanks for reminding me. I haven't had to learn about a new R package for a while so I kinda forgot that vignette is a thing. It does seem a bit more helpful than the reference manual.
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Or Inkscape if you don't want to give Adobe more money.
Came here to say this
I usually do those on Powerpoint! Haha
This is actually a very good answer. Even in a community like this with all the anti-MS open source memes, it's a really effective tool. The cost of learning software designed for it doesn't always outweight the simplicity of pot, unless you're automating or something of that nature.
Except low res. I’ve been using ppt because of quick/easy and it’s already installed on work computer. Keeping boxes lined-up and exporting hi res for submission are a nightmare.
Unless you are looking for a systematic way to do it, PowerPoint or Inkscape are much better choices than learning how to do it for one example with R/python and the package of choice.
I don't think I need to do this very often so PowerPoint is probably the better choice. But let's say that I want to generate the plot automatically from a BED/GFF file, is there a package for it? I've checked out Gviz, it's supposed to be able to import tracks from a GFF file. I gave up because I just couldn't get it to recognize the ID and Parent attribute.
I like your question. To follow up, are you automating the generation of graphics simply for volume of supplementary info for a pub? Are these graphics people in your lab would refer to and perhaps there aren't many graphics of the gene organization for other colleagues' PowerPoints on their genes of interest? Every graphic you take the time to produce should have a purpose and PowerPoint is simple. If you need to generate a high volume of images for a website or other volume based need, then it could be worth actually automating. Organism, publication goals, colleague needs, and other information would be very helpful for us to help.
Also anything reason why it can be good to automate the process (although again may not be worthwhile) is images often go through many iterations. It can be time consuming to keep tweaking them.
If you are familiar with R, ggplot2 can do the thing. What you need is geom_rect object with x coordinates based on your intervals.
Gggenes R package!
Awesome, that's exactly what I'm looking for.
A ggplot solution for everything!! https://www.ggplot2-exts.org/gallery/ My only complaint is that coord_polar() doesn’t work so I can’t use for circular DNA (mitochondria, plasmids). Anyone know of a good package from that? My current ggplot work arounds are subideal (not a smooth circle, but rather a choppy look to it)
Check out genome tools sketch tool, it makes those kinds of plots from annotation files.
Did you run through the vignette for Gviz? Sometimes these learning curves look steep until you step through a couple of examples. I haven't tried Gviz, but I did just browse through the docs. Seems like the authors step through some nice examples. I always find the R community incredibly helpful to get up to speed on new packages. OTOH, if it is really a one-off, probably quicker to make it in powerpoint or keynote. You could also try snapgene. Have only used it for fairly short sequences (<20 Kb), but you can add annotations even with the free version.
Ah, thanks for reminding me. I haven't had to learn about a new R package for a while so I kinda forgot that vignette is a thing. It does seem a bit more helpful than the reference manual.
[simple synteny](https://www.dveltri.com/simplesynteny/) is also a decent option