[R] problem with plotting clustered data with convex hull using ggfortify

Rui Barradas
Sun, 24 Oct 2021 22:32:03 -0000

Hello,

R 4.1.1 on Ubuntu 20.04.3 LTS.

I can reproduce this error. It happens with ggfortify 0.4.12 but not
with 0.4.11.

First ggfortify 0.4.11, notice the warnings.


rui at rui:~$ R -q -f rhelp.R
 > library(ggfortify)
Loading required package: ggplot2
 > library(cluster)
 >
 > autoplot(fanny(iris[-5], 3), frame = TRUE)
Warning messages:
1: `select_()` was deprecated in dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
2: `group_by_()` was deprecated in dplyr 0.7.0.
Please use `group_by()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
 > packageVersion("cluster")
[1] ?2.1.2?
 > packageVersion("ggfortify")
[1] ?0.4.11?
 >
 > sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS
[...]


#---------------

Now ggfortify 0.4.12, notice that the errors are gone but there's a
message, probably printed with cat().



rui at rui-p6550pt:~$ R -q -f rhelp.R
 > library(ggfortify)
Loading required package: ggplot2
 > library(cluster)
 >
 > autoplot(fanny(iris[-5], 3), frame = TRUE)
Adding missing grouping variables: `cluster`
 > packageVersion("cluster")
[1] ?2.1.2?
 > packageVersion("ggfortify")
[1] ?0.4.12?
 >
 > sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS
[...]


One problem was fixed, another showed up.
You should contact the package maintainer.


Hope this helps,

Rui Barradas


?s 21:57 de 24/10/21, Karl Schilling escreveu:
> Dear all:
>
> I have some data that I want to cluster and display as groups surrounded
> by convex hulls. Here, i use the iris data as an example:
>
> library(ggfortify)
> autoplot(fanny(iris[-5], 3), frame = TRUE)
>
> I used this code before, about a year ago, and then it resulted in data
> surrounded by convex hulls., just as may be seen in the description of
> ggfortify here:
>
>
>
http://rstudio-pubs-static.s3.amazonaws.com/53162_cd16ee63c24747459ccd180f69f07810.html
>
>
>
> Presently, no hulls are drawn; instead some line is projected on each
> cluster.
>
> I found out that there is an addition to autoplot command, "frame.type
=
> c("convex", "norm", "t"). Whereas
""norm" and "t"? give confidence
> ellipses as expected, "convex" results in a straight line as
mentioned
> above.
>
> Any help would be appreciated.
>
> Best
>