how to draw group membership probabilities into scatter plots

[genetist]

Hi
I have csv file having 4 columns 1st clum is members and remaining columns are their group membership probabilities. Now i would like to create scatter plot like in the attached file, is it possible with ggplot2 in R? any help in this regard will be highly appreciated.
Thanks in advance

[dromano]

How was the plot you shared made?

[FJCC]

Here is a simple example of a similar plot. What determines the x and y positions on your plot?

library(ggplot2)
library(dplyr)
#Invent data
DF <- data.frame(Group = c("A","A","A","B","B","B","C","C","C"),
                 X = c(0.13,0.23,0.27,0.55,0.52,0.43,0.71,0.74,0.65),
                 Y = c(0.32,0.3,0.22,0.44,0.40,0.53,0.75,0.68,0.7))
#Calculate group means
DF <- DF |> group_by(Group) |> 
  mutate(GrpMeanX = mean(X), GrpMeanY = mean(Y))

DFmeans <- DF |> group_by(Group) |> summarize(MeanX = mean(X), MeanY = mean(Y))

#Plot
ggplot(DF) +
  geom_segment(aes(x = X, y = Y, xend = GrpMeanX, yend = GrpMeanY, color = Group)) + 
  geom_point(aes(x = X, y = Y, color = Group)) + 
  geom_label(aes(x = MeanX, y = MeanY, label = Group), data = DFmeans)

[genetist]

Hi dromano
Thanks for your message. I can create example shown graph using this code

library(adegenet)
x<-input_file
x1<-as.data.frame(t(x))
gen<-as.genlight(x1)
grp<-find.clusters(gen,max.n.clust = 10) 
dapc1<-dapc(gen,grp$grp) # up to here i have data shown as in my example
scatter(dapc1) # here i want to plot the clusters using dataframe.

i have individuals with membership probabilities not exactly as groups i need to group them based on similar membership probabilities. I hope i explained you well.

[genetist]

Dear FJCC
Thanks for your help to my request. Your code is working good, but i have individuals with membership probabilities not exactly as groups i need to group them based on similar membership probabilities of groups from Q1 to Q3, other than this your code working well.
Thanks

[dromano]

Could you describe or share the contents of x1? To share them, you could execute the following lines:

sink("x1.txt")       # directs output to a new file called "x1.txt"
dput(x1[1:20, 1:20]) # writes code for recreating a few rows and columns of x1  to "x1.txt"
sink()               # restores output back to the console

and then

• open the file "x1.txt" and copy the output
• paste the output here, between a pair of triple backticks like this:

```r
[<-- paste here]
```