I'm currently trying to reproduce some of our graphs in R.
At the moment we use Excel to produce our graphs and 1 of the options in Excel is the use of gradient colors on the axis. I have added some pictures as an example.
My question is if a similar option is available in R (in ggplot). I can't find any useful information about this issue on the web. Thanks in advance for any response!
Greetings, Erik
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I am trying to plot gsea similar to image as given below:
the tutorial does not give you such plots. So I tried the github link.
But it failed to generate the similar plot
I checked both gseaplot2{enrichplot} and plotEnrichment{fgsea} and found no options to automatically add the group names. It might be a good idea to just add the names after exporting to Adobe Illustrator. Would be happy to hear other ideas though if anyone else knows a better way.
I am trying to duplicate a circular barplot made with ggplot2 into ciclize as follows:
While I can bring it into a scatterplot and add a regression:
The visualization as barplot interests me more. However I have not found any similar example in the circlize guide or any example. I have tooled with the circos.polygon however drawing each bar seems not the best solution. Thus, I wonder if someone has toyed with this already, while no specific subject existis in stackoverflow.
I contacted Zuguang Gu on twitter and he was kind enough to make a wraper function for circlize. He posted the details here:
https://jokergoo.github.io/circlize/reference/circos.barplot.html
I really like ggplot2 but the level of detail and easy handling for circular barplots made me look for an answer using circlize.
Thanks to all that answered.
I would need create a chart like the one on the picture. I don't want to draw it by hand, since I need more of them. I prefer R CRAN for drawing charts, but would do also any other programming or plotting program. If possible pdf or eps outputs are preferable. Does anybody have an idea, what type of chart, or which R (or other SW) package would support something like that?
I have found the solution. Orange software package makes the charts.
https://docs.orange.biolab.si/3/data-mining-library/reference/evaluation.cd.html
This idea has been spurred by this work at Five Thirty Eight.
I'm not entirely sure that they used R, but the chart appears in a similar fashion to their other data viz. I looked around here, but couldn't find anything directly relating to this.
Is this kind of plot possible using ggplot?
Thanks for any and all help!
They do use R but their ggplot2 theme is semi-proprietary and they don't say what they use. People have attempted to recreate the theme
https://github.com/jrnold/ggthemes
After the graphs are created it then goes through an illustrative step to bring graphs together and make them more of a story.
I'd like to create a heat map in R that I want to use on a website. I stumbled upon the SVGAnnotation package which seems to be very nice to process SVG graphics in R to make them more interactive. First, I was planning to add tool tips for each cell in the heatmap - if the user hovers over the cell, the value of this cell should pop up. However, I am fighting with SVGAnnotation for more than 3 hours now, reading and trying things, and I can't get it to work.
I would appreciate any help on the SVGAnnotation tool tip function. But I would also very much appreciate alternatives to SVGAnnotation to add some activity to my R SVG heatmap.
So, what I have got so far looks like this:
library(SVGAnnotation)
data(mtcars)
cars <- as.matrix(mtcars)
map <- svgPlot(heatmap(cars))
addToolTips(map, ...) # problem
saveXML(map, "cars.svg")
My problem is the addToolTips function itself, I guess. Intuitively, I would simply insert the data matrix, i.e., cars, but this does not work and R gets stuck (it's calculating, but doesn't return anything, I waited 50 minutes)
EDIT:
After some more online research, I found a good example of what I want to achieve: http://online.wsj.com/article/SB125993225142676615.html#articleTabs=interactive
This heat map looks really great, and the interactive features (tool tips) work very well. I am wondering how they did that. To me, it looks like the graphic was done in R using the ggplot package.
I wrote a command line tool that can do exactly that if you are still interested to add tool tips to your heat map. It runs in Windows/Linux/MacOS terminals. All you need as input is the heat map as svg file and the data table/matrix that you used as input to create your heat map as csv or other text file.