ggbiplot | A biplot based on ggplot2 | Data Visualization library
kandi X-RAY | ggbiplot Summary
kandi X-RAY | ggbiplot Summary
An implementation of the biplot using ggplot2. The package provides two functions: ggscreeplot() and ggbiplot(). ggbiplot aims to be a drop-in replacement for the built-in R function biplot.princomp() with extended functionality for labeling groups, drawing a correlation circle, and adding Normal probability ellipsoids.
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QUESTION
When I do the below code on my data, since there are 35 variables the resulting plot is almost useless because of all the overlap. I can't seem to find anywhere that would give me the list of data that's used to make the plot. For instance, I have a factor called avg_sour that has a direction of about 272 degrees and a magnitude of 1. That's one of the few I can actually see. If I had this data in a table, however, I could see clearly what I'm looking for without having to zoom in and out every time. Add to that the fact that this is for a presentation, so I need to be able to make this visible quickly, without them looking at multiple things--but I think I could get away with a crowded graph and a table that explained the crowded portion. Seems like it ought to be simple, but...I'm afraid I haven't found it yet. Any ideas? I can use any package I can find.
...ANSWER
Answered 2021-Oct-19 at 02:07If your xD4PCA
is from prcomp
function, then $rotation
gives you eigenvectors. See prcomp function - Value.
You may manually choose and add arrows from xD4PCA$rotation[,1:2]
I was working on this with sample data ir.pca
, which is just simple prcomp
object using iris
data, and all these jobs are based on source code of ggbiplot.
QUESTION
biplot<-ggbiplot(pcobj = PCA,choices= c(1,2),scale = 1,groups = Fdata$Tissue,ellipse = TRUE)+
geom_vline(xintercept = 0, linetype = 3)+geom_hline(yintercept = 0, linetype = 3)
...ANSWER
Answered 2021-Oct-13 at 00:07try add geom_point(aes(shape=factor(something)))
. For an example of iris
data,
QUESTION
I'm currently running principal component analysis. For the interpretation I want to create a profile (pattern) plot to visualize the correlation between each principal component and the original variables. Is anyone familiar with a package or code to create this in R? I'm using the prcomp() function in R.
See examples:
https://canadianaudiologist.ca/predicting-speech-perception-from-the-audiogram-and-vice-versa/ https://blogs.sas.com/content/iml/2019/11/04/interpret-graphs-principal-components.html
This is similar data to my db:
...ANSWER
Answered 2021-May-27 at 09:30using your data I did this:
QUESTION
I need some help to modify my R script that could assign different color to each group. I always need to specify color name/code manually [e.g., scale_fill_manual(values = c("grey", "red", "yellow", "green"))].
Complete R script is here
...ANSWER
Answered 2021-Apr-17 at 20:13scale_color_manual(values=ir.species)
scale_color_manual(values=1:20) # assumes 20 colours
QUESTION
I need some help to get PC3 and PC4 for my data.
...ANSWER
Answered 2021-Feb-07 at 16:20By including ggbiplot(ir.pca, choices = c(3,4), obs.scale.... we can get PC3 and PC4.
QUESTION
I have a PCA plot that ive been working on a while now (I am not very good at R but this is teaching me a lot, just trying to make this one plot). I am now at the stage where the plot looks how we want it, now we just want to draw ellipses around the replicates. (see plot below)
Ideally, the ellipses would have the border colour the exact same colour and be filled in with a mostly transparent version of that same colour (see example plot below)
Many people have suggested using ggbiplot, which i tried but i found the manual very sparse in detail and i didnt really understand how to control the plot. To generate the plot i used the following code:
...ANSWER
Answered 2020-Nov-05 at 19:41Good suggestion by @Axeman, so you can use geom_polygon():
QUESTION
I use ggbiplot
regularly and can control every aspect of the plot produced using ggplot2
tools, since it inherits from ggplot2
...
In ggplot2
, I usually control the number of columns in the legend with a line of the form:
ANSWER
Answered 2020-Jul-23 at 10:13It'd be simpler to include the ncol = 2
in the first call to guide_legend()
. I.e.
QUESTION
How can I added the Species classifier next to the centroid in this PCA plot.
Code:
...ANSWER
Answered 2020-Jun-23 at 09:56I'm not sure why you would need the ggpubr and ggbiplot packages in this case. You can do this with just ggplot2 (and data.table which you already used in your example).
QUESTION
I am struggling with changing the loading labels of biplot. I used prcomp function to run PCA and ggbiplot. I've tried to change it with loading.label.label = c("a","b","c","d")
, but it didn't work. I have attached my code and plot below.
ANSWER
Answered 2020-Jun-18 at 07:25Not sure you can do this with the ggbiplot
function. A workaround would be to change the names in the pca
object like this:
QUESTION
I would like to plot the distribution of multiple columns of my data set. It has over 820.000 rows and 18 columns. I want to plot all columns except the columns with the dummy variables. I have already been able to create a graphic. But I want to have the values of the x-axis on the y-axis because these are the column values and I want to display their distribution for each column.
1. Definition of the path ...ANSWER
Answered 2020-Mar-19 at 16:00You don't need to combine your dataframe all over again. What you need is either a density plot or histogram.
Also as good practice, load only the packages required for plotting, in this case it would be maybe ggplot2 and tidyr.
For example, I just used an example with 5 of the column names I can see in your data:
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