What I would like to do is make a series of plots that combine an image with a scale that is related to the height of the image, but is multiplied by a factor.
So far I've been able to make a plot using the following code:
library(imager)
im <- load.image("ZAB17_4.png")
plot(im)
Image is attached here
But what I would like to do is to have the y-axis be scaled by a value:
pixel_size <- 0.0596
I would also get rid of the x-axis. (xaxt="n" doesn't seem to do the trick). Ideally, I would like the Y-axis to be directly adjacent to the image. I've been trying to poke around with scales in the plot function, but haven't found what I need to do this, but I'm sure there is a simple solution.
*Edited to add image. I should note that the goal is really just to add a scale to the image. The pixel size represents the size of each pixel in reality in mm. I basically want to add a ruler along the side of the image. Maybe r is not the best tool for this, but I plan to also plot data taken from the imaged object and plot it alongside.
Any help is appreciated.
Related
I am trying to create a figure of a map of a continuous trait onto a phylogenetic tree using the ape and phytools packages in R for a publication. An example code of what I am trying to produce is as follows:
library("ape")
library("phytools")
orig_tree<-rtree(n=350)
plot(orig_tree)
values<-data.frame("residuals"=runif(350,min=-1,max=1),row.names=orig_tree$tip.label)
values<-setNames(values$residuals,rownames(values))
residualsignalfit<-fastAnc(orig_tree,values,vars=TRUE,CI=TRUE)
obj<-contMap(orig_tree,values,plot=FALSE)
plot(obj,type="fan",fsize=.1,lwd=0.5)
The only difference is the terminal of the branches are all the same length because they are all living taxa, but this works well enough to illustrate the problem I am having. I have a large number of taxa in this tree, and as a result I have to shrink the text down fairly small using the fsize= argument to make them legible. However, as you can see from the example code, doing so causes the ends of each species name to be obscured by the outline for the phylogenetic tree. I have tried removing the outline but it makes the heatmap of the phylogeny very hard to read. I have been unable to find any way to reduce the thickness of the outline, it seems to be automatically generated.
I also tried adding the cex command to plot(obj...), but it has no effect on the produced tree at all.
What I am trying to figure out how to do is how to position the tip labels in order to make them more legible and not covered up by the outline for the tree. I cannot simply add a space in front of each terminal using the dplyr mutate function or something like that because the position of the taxon name is not always consistent, sometimes the left side of the name is attached to the tip and other times it is the right side. I have tried not plotting the data as a fan, but this ends up creating a figure with a huge amount of dead space due to the fact I have some very deep splits within the tree (basically plotting the figure as a right-facing tree results in half of the figure being dead space because my taxa diverged in the Mesozoic but only speciated after the K-T boundary).
Instead of shrinking the text down, you can scale the tree up. You can export the plot as image with a specific width and height. Setting both to 20 should make all tip labels legible.
Something like
setEPS()
postscript("output.eps", width = 20, height = 20)
plot(obj,type="fan",lwd=0.5)
dev.off()
This saves the plot to output.eps instead of showing it in the default viewer. So it is not restricted by the screen size. You still need to fiddle around with the best values of lwd and fsize, but in my experience it is much easier, when you have a big canvas.
Edit: Sorry, the unit of width and height is inches not pixels. So rather set it to 10 or 20.
I have a plot with 50 categories(states) that show on my X axis, but in my output they are on top of each other. I want my plot to be spread out engough/large enough that there is no overlap and you could determine the state value from the next.
NOTE: i used the coord_flip command, so I know that my X-axis is actually my Y in image and vice versa. I am just wondering what function I would use to fix problem.
You can always change the size of the text via themes(axis.text.x=element_text(size=...))...
But the easy answer here is that your plot will change appearance based on the aspect ratio. When you view in Rstudio, you can adjust the size of your plot and you'll see the rearrangement. Additionally, when you save, the plot, play around in particular to the height and width to get the ratio you want. ggsave('filename.png', width=??, height=??).
I'm using corrplot in R to plot the correlation matrrix. For some reason, the edges of the circles in the plot seems missing some pixels. The plot overall looks very rough. Please see the graph I plotted:
enter image description here
But the example I followed shows the plot is supposed to be like this:
enter image description here
My initial guess was dpi and scaling issue because I use a 4K display. I tried changing the resolution and size of the plots but it doesn't work.
Thank you so much for your help.
How do I adjust the overall size of a ggplot?
I'm using Shiny, thus, I'd like to control the size of my plot. I'd like one of my plots to be the size of a postage stamp. And, I'd like the plot next to it to be huge.
From what I can tell, no matter how much I play with scale_x_continuous or xlim or cartesian_coord or whatnot, I'm still stuck with a ggplot that has made up it's own mind on how big it wants to be. I can squish down the amount of ink within the size of the plot, or I can fill up the insides of the plot by using various attributes, but I can't change the number of pixels the plot takes up on my screen.
How can I specify the exact number of pixels I would like my plot to be?
I don't know shiny, but maybe this helps,
library(grid)
print(qplot(1,1), vp=viewport(width=unit(114,"points"), height=unit(1.4,"inch")))
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