I'm wondering how I can make figures or plots like this one in Sage, if it's possible:
Thanks very much.
Related
I am implementing a R shiny with a plot panel implemented by library(ggplot2). If there are 12 plots, the layout looks great. Please check below.
12-plot layout
However, if I increase the plot number to 70, then each plot looks being compressed (pls see below). Is that possible I can keep the size of each plot fixed? Thank you so much!
enter image description here
Is there another way to approach this? For instance, can you group your data by two categorical variables and use on for colouring and the other for facetting? In that way, you may be able to reduce the number of facets, and stick with the larger facet size, while still conveying all relevant information? 70 facet plots is a lot!
Is this more of a QC thing? For QC, I tend to break it into groups by condition as Paul was suggesting. The reason is that within a condition, things should be really similar. Outside a condition, all bets are off. When I do this for genomics data, I tend to use “pairs” customized to my liking.
What don’t you like about the 70 sample display? Simply the change in aspect ratio? IMO, these are the things I don’t like about ggplot. You can make these plots using base R and then place them on a page manually using par or layout. For that matter, you can do the same with ggplot and use ggarrange or a different manual layout function to place the plots. All wrapped in a for or apply of course.
The other things I like to do when I have a LOT of QCs to look through is create a movie. I can use the forward/back buttons and go through a lot quickly. I like the idea of having this in a dashboard, nice one!
you could also try coord_fixed(ratio= ), not sure if that will work with faceting or not
Finally, I have made a movie-like visualization for those 70 plots using the plot_ly function in R package "plotly".
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 am trying to make the following plot (which I made in R) using ggplot2. How do I go about doing this? (The plot has a finer resolution from 0 to 10, but coarser resolution from 10 onwards.) know how to do this in R, but I am not sure how to proceed with this in the case of ggplot2. Here is the figure obtained using base R.
To make things useful, note that i don't have that much interest in hanging on to the right-hand y-axis.
Also, I would like to do a similar task on a pair of barplots (have the same scale, and only one y-axis. I am hoping that that approach is similar.
I would also be open to other suggestions that would make a similar plot conveying the information similarly or better.
Many thanks for suggestions!
I'm working on a really complicated heatmap figure in R. heatmap.2 from the gplots package is not enough for me, because I want multiple sidebar annotations, such as the heatmap.3 function permits: https://www.biostars.org/p/18211/
Here's my specific plot so far:
When I have multiple sidebar annotations on this heatmap, though, they need to be properly labeled with a legend. The legend quickly becomes unwieldy and starts bleeding off the plot or into other labels on the plot, depending on where I choose to place the legend.
I've tried using the ncols option when placing the legend at the bottom of the plot but the legend contains information about several factors worth of metadata, and I want a separate column in the legend to denote each sidebar's worth of metadata. As far as I know there is no option in the legend command to permit this functionality, so I'm interested in hearing potential ways around this.
Alternatively, I am also open to the idea of simply generating a legend image with R separately if anyone knows how to do this.
Thanks!
These days I am extensively using R to scatter plots.
Most of the plotting is concerned with image processing,
Recently I was thinking of plotting the scatter plots over an image.
For example, I want something like this,
The background needs to be filled with my image. With a particular scale.
And I should be able to draw points (co-ordinates) on top of this image ...
Is this possible in R?
If not, do you guys know of any other tool that makes this easy ...
I'm not 100% sure what you have in mind, but I think first you want to load and plot an image in R. You can do that with the ReadImages package:
picture <- read.jpeg("avatar.jpg")
plot(picture)
Then you can do a scatter plot on top of it:
points(runif(50,0, 128), runif(50,0,128))
A step-by-step tutorial to this kind of plotting is in the R-wiki