I want to use the shown plot and generated it with plot_model(model, type="int") using sjPlot. But as you can see since one of the graphs overshoots by a lot the others can't be read properly. So i would like to scale the y-axis logarithmicly. How can i achieve this ? (R beginner so maybe i am missing the obvious)
Related
I am new to R and I have been using chromoMap library in R to visualize annotation plots and visualizing the feature-associated data. It's a great library and produces great charts. However, I was not able to find any option for changing the x-axis label from length (bp) to anything else. Because of this, I am not able to use any of the produced charts. It sounds like a small issue, but it totally affects the usability of this great package. I followed this tutorial link and produced the below chart. In my chart and all the samples, the x-axis label is fixed and this is my problem and I am looking for a way to just change it.
library(chromoMap)
chr_file_1 = "chr_file_without_centromere.txt"
anno_file_1 = "annotation_pos.txt"
chromoMap(chr_file_1,anno_file_1)
I am wondering if anybody has the same experience ?? This package produces output as a htmlwidget object and therefore I could not change the x-axis lable. Is there any way to modify a htmlwidget object? or Any way to change this bp to something else??
I’m using the metafor package to create Forest plots in R. I’d like to add text to my plots to create labels using the text() function. I’m wondering what the simplest way is to determine the x,y coordinates of where I want my text to go. Currently I just guess and see how it looks and then edit as necessary. Is there a way to overlay a grid over my plot or something to guide me (and then remove it after)?
Thank you!
Start by saving what forest() returns:
x <- forest(res)
And then take a look at x. Among other things, it contains xlim and ylim, which are the x-axis and y-axis limits. Try this:
abline(v=x$xlim)
abline(h=x$ylim)
Also useful:
text(x$xlim[1], x$rows, x$rows, xpd=NA)
I hope this helps.
I have a plotting problem with curves when using mixtools
Using the following R code
require(mixtools)
x <- c(rnorm(10000,8,2),rnorm(10000,18,5))
xMix <- normalmixEM(x, lambda=NULL, mu=NULL, sigma=NULL)
plot(xMix, which = 2, nclass=25)
I get a nice histogram, with the 2 normal curves estimated from the model superimposed.
The problem is with the default colours (i.e. red and green), which I need to change for a publication to be black and grey.
One way I thought to doing this was first to produce the histogram
hist(xMix$x, freq=FALSE, nclass=25)
and then add the lines using the "curve" function.
....... but I lost my way, and couldn't solve it
I would be grateful for any pointers or the actual solution
thanks
PS. Note that there is an alternative work-around to this problem using ggplot:
Any suggestions for how I can plot mixEM type data using ggplot2
but for various reasons I need to keep using the base graphics
You can also edit the colours directly using the col2 argument in the mixtools plotting function
For example
plot(xMix, which = 2, nclass=25, col2=c("dimgrey","black"))
giving the problem a bit more thought, I managed to rephrase the problem and ask the question in a much more direct way
Using user-defined functions within "curve" function in R graphics
this delivered two nice solutions of how to use the "curve" function to draw normal distributions produced by the mixture modelling.
the overall answer therefore is to use the "hist" function to draw a histogram of the raw data, then the "curve" function (incorporating the sdnorm function) to draw each normal distribution. This gives total control of the colours (and potentially any other graphic parameter).
And not to forget - this is where I got the code for the sdnorm function - and other useful insights
Any suggestions for how I can plot mixEM type data using ggplot2
Thanks as always to StackOverflow and the contributors who provide such helpful advice.
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 made a plot in R and I want to repeat all the commands (like plot(), legend() or line()) that were carried out for this plot, with some minor changes. For example I want to set the axes to logarithmic scale and change the title of the plot.
In gnuplot I would use the replot command.
plot ...
set title "The same plot with logarithmic axes"
set logscale
replot
Is something like this possible in R. The only thing that comes to my mind of doing this (besides changing the values manually and re-run the lines of codes) would be setting up a function, that asks for all parameters that might be changed by the user.
Thanks for your help,
Sven
R uses a pen and paper graphics model - once the plot has been drawn on the device that is it. If you want to change some aspect of the plot, you need to replay the graphics function calls that produce the plot with the changes made to the code.
Depending on what you are really doing there are two options:
If this is just for you, write code in a text editor / IDE that knows R and can send chunks of code at a time to R. That way the code to produce the figure is recorded in a separate script which you can paste into/send to R making the changes you need each time to the script.
If you are going to be doing this often, then write yourself a wrapper plotting function that encapsulates the plot code you want but allows you to pass in arguments to alter the aspects you want.
Lattice and ggplot2 are a little different as they are based on grid graphics and create objects that when printed produce a plot on the device. One can manipulate that object to alter what is drawn, and with grid one can push and pop things on to / off a viewport.