How can I add tags to my points on a PCA with ggplot2?

Manu2592 · March 3, 2020, 9:17pm

Hi, I made a PCA with ggplot2, however I want my PCA points to have a name, what function could I use. Thank you
Taxon MOPF MA RA TV GT
1 Andesiops 75 25 0 0 detritívoro
2 Meridialaris 5 95 0 0 herbívoro
3 Polycentropus 20 0 80 0 depredador
4 Austrelmis 93 7 0 0 detritívoro
5 Prionocyphon 40 0 60 0 depredador
6 Neoplasta 98 2 0 0 detritívoro
7 Gigantodax 65 15 20 0 detritívoro
8 Simulium 30 65 5 0 herbívoro
9 Tipula 30 0 0 70 herbívoro
10 Alotanypus 60 20 20 0 detritívoro
11 Pentaneura 35 5 60 0 depredador
12 Corynoneura 15 85 0 0 herbívoro
13 Cricotopus 90 10 0 0 detritívoro
14 Tanytarsus 95 5 0 0 detritívoro
15 Podonomus 25 75 0 0 herbívoro
16 Podonomopsis 85 15 0 0 detritívoro
17 Parochlus 95 5 0 0 detritívoro

williaml · March 3, 2020, 9:29pm

Here is a reprex of your data. Have you got your ggplot code?

df <- tibble::tribble(
           ~Taxon, ~MOPF, ~MA, ~RA, ~TV,           ~GT,
      "Andesiops",    75,  25,   0,   0, "detritívoro",
   "Meridialaris",     5,  95,   0,   0,   "herbívoro",
  "Polycentropus",    20,   0,  80,   0,  "depredador",
     "Austrelmis",    93,   7,   0,   0, "detritívoro",
   "Prionocyphon",    40,   0,  60,   0,  "depredador",
      "Neoplasta",    98,   2,   0,   0, "detritívoro",
     "Gigantodax",    65,  15,  20,   0, "detritívoro",
       "Simulium",    30,  65,   5,   0,   "herbívoro",
         "Tipula",    30,   0,   0,  70,   "herbívoro",
     "Alotanypus",    60,  20,  20,   0, "detritívoro",
     "Pentaneura",    35,   5,  60,   0,  "depredador",
    "Corynoneura",    15,  85,   0,   0,   "herbívoro",
     "Cricotopus",    90,  10,   0,   0, "detritívoro",
     "Tanytarsus",    95,   5,   0,   0, "detritívoro",
      "Podonomus",    25,  75,   0,   0,   "herbívoro",
   "Podonomopsis",    85,  15,   0,   0, "detritívoro",
      "Parochlus",    95,   5,   0,   0, "detritívoro"
  )

FAQ: How to do a minimal reproducible example ( reprex ) for beginners Guides & FAQs

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…

andresrcs · March 3, 2020, 9:56pm

If you are just looking for a pointer you can use geom_text () or geom_label () but if you need specific advice, then I recommend you to provide a reproducible example as requested by William, since it seems you are a fellow Peruvian (because of your university), maybe you prefer the Spanish version of the reprex guide

Pregunta Frecuente: ¿Cómo hacer un ejemplo mínimo reproducible (reprex)? - para principiantes Guides & FAQs

Un ejemplo mínimo reproducible consiste de los siguientes puntos: Un conjunto de datos mínimo que permita reproducir el problema. El mínimo código ejecutable necesario para reproducir el problema, que pueda ser ejecutado con el conjunto de datos brindado y que incluya la información necesaria sobre los paquetes utilizados. Vayamos rápidamente sobre cada uno de estos puntos con ejemplos: Conjunto de Datos Mínimo (Datos de Muestra) Usted necesita proporcionar un conjunto de datos que sea lo suficientemente pequeño para ser pegado (razonablemente) en una publicación, pero lo suficientemente grande para reproducir el problema. Digamos, a manera de ejemplo, que usted está trabajando con el…

Manu2592 · March 3, 2020, 11:23pm

library(ggfortify)
setwd("C:/Users/M4NU.51LV4/Desktop/Pca en R")

chi=data.frame(pca2)

chicucha<- chi[c(1, 2, 3, 4)]
autoplot(prcomp(chicucha))
autoplot(prcomp(chicucha), data = chi, colour = 'GT')
autoplot(prcomp(chicucha), data = chi, colour = 'GT', loadings = TRUE)

Manu2592 · March 4, 2020, 1:43pm

Thanks, I managed to put the names, but these overlap, is there any code to avoid that?

Manu2592 · March 4, 2020, 1:44pm

Thanks, I managed to put the names, but these overlap, is there any code to avoid that

andresrcs · March 4, 2020, 2:17pm

There is an extention package called ggrepel that you can use for that.

dromano · March 4, 2020, 3:19pm

You could also try including the argument check_overlap = TRUE inside of your geom_text() call (but outside of aes()), and see if that helps.

Manu2592 · March 4, 2020, 4:40pm

how could I add it in the following code?

autoplot(prcomp(chicucha), data = chi, colour = 'GT', label = TRUE, loadings = TRUE)

Manu2592 · March 4, 2020, 4:40pm

how could I add it in the following code?

autoplot(prcomp(chicucha), data = chi, colour = 'GT', label = TRUE, loadings = TRUE)

andresrcs · March 4, 2020, 5:49pm

There is no need to repeat your posts we all can see them.

As I said before, if you need more specific help, please provide a proper REPRoducible EXample (reprex) illustrating your issue.

dromano · March 4, 2020, 6:03pm

Could you post the table chicucha for us? (The data you provided earlier, and which @williaml kindly posted, won't allow us to reproduce the steps you took.)

The easiest way to do this is to use the dput() function and post its output between a pair of triple backticks (```) like this:

```
[paste output of dput(chicucha) here]
```

If chicucha is big table, then you should use the output of dput(chicucha %>% slice(1:50)) instead -- this would be a big help to us in trying to help you.

Manu2592 · March 4, 2020, 7:19pm

Thank you very much for your support, I am new to the R environment, thanks for your answers, I hope this time I do it well

dput(chi)

chi
library(ggfortify)
library(ggplot2)
rownames(chi)<- chi$Taxon
chicucha<- chi[c(2, 3, 4, 5)]
chicucha
autoplot(prcomp(chicucha))
autoplot(prcomp(chicucha), data = chi, colour = 'GT')
autoplot(prcomp(chicucha), data = chi, colour = 'GT', label = TRUE, loadings = TRUE)

dromano · March 4, 2020, 7:25pm

OK, in that case, you should post the output from dput(chi), meaning, you should copy the output, and paste it here between triple backticks (```), like this,

```
[paste output of dput(chi) here]
```

You need the triple backticks so we can copy it easily.

Manu2592 · March 4, 2020, 7:30pm

dput(chi)
chi

                         "Austrelmis", "Prionocyphon", "Neoplasta", "Gigantodax", "Simulium", 
                         "Tipula", "Alotanypus", "Pentaneura", "Corynoneura", "Cricotopus", 
                         "Tanytarsus", "Podonomus", "Podonomopsis", "Parochlus"), MOPF = c(75, 
                                                                                           5, 20, 93, 40, 98, 65, 30, 30, 60, 35, 15, 90, 95, 25, 85, 95
                         ), MA = c(25, 95, 0, 7, 0, 2, 15, 65, 0, 20, 5, 85, 10, 5, 75, 
                                   15, 5), RA = c(0, 0, 80, 0, 60, 0, 20, 5, 0, 20, 60, 0, 0, 0, 
                                                  0, 0, 0), TV = c(0, 0, 0, 0, 0, 0, 0, 0, 70, 0, 0, 0, 0, 0, 0, 
                                                                   0, 0), GT = c("detritívoro", "herbívoro", "depredador", "detritívoro", 
                                                                                 "depredador", "detritívoro", "detritívoro", "herbívoro", "herbívoro", 
                                                                                 "detritívoro", "depredador", "herbívoro", "detritívoro", "detritívoro", 
                                                                                 "herbívoro", "detritívoro", "detritívoro")), class = "data.frame", row.names = c("Andesiops", 
                                                                                                                                                                  "Meridialaris", "Polycentropus", "Austrelmis", "Prionocyphon", 
                                                                                                                                                                  "Neoplasta", "Gigantodax", "Simulium", "Tipula", "Alotanypus", 
                                                                                                                                                                  "Pentaneura", "Corynoneura", "Cricotopus", "Tanytarsus", "Podonomus", 
                                                                                                                                                                  "Podonomopsis", "Parochlus"))```¨

library(ggfortify)
library(ggplot2)
rownames(chi)<- chi$Taxon
chicucha<- chi[c(2, 3, 4, 5)]
chicucha
autoplot(prcomp(chicucha))
autoplot(prcomp(chicucha), data = chi, colour = 'GT')
autoplot(prcomp(chicucha), data = chi, colour = 'GT', label  = TRUE, loadings = TRUE)

dromano · March 4, 2020, 8:00pm

That's better! But you cut off part of the output from dput(chi) -- could you try again and only paste the output of dput(chi) and don't include any other code?

Manu2592 · March 4, 2020, 8:05pm

                         "Austrelmis", "Prionocyphon", "Neoplasta", "Gigantodax", "Simulium", 
                         "Tipula", "Alotanypus", "Pentaneura", "Corynoneura", "Cricotopus", 
                         "Tanytarsus", "Podonomus", "Podonomopsis", "Parochlus"), MOPF = c(75, 
                                                                                           5, 20, 93, 40, 98, 65, 30, 30, 60, 35, 15, 90, 95, 25, 85, 95
                         ), MA = c(25, 95, 0, 7, 0, 2, 15, 65, 0, 20, 5, 85, 10, 5, 75, 
                                   15, 5), RA = c(0, 0, 80, 0, 60, 0, 20, 5, 0, 20, 60, 0, 0, 0, 
                                                  0, 0, 0), TV = c(0, 0, 0, 0, 0, 0, 0, 0, 70, 0, 0, 0, 0, 0, 0, 
                                                                   0, 0), GT = c("detritívoro", "herbívoro", "depredador", "detritívoro", 
                                                                                 "depredador", "detritívoro", "detritívoro", "herbívoro", "herbívoro", 
                                                                                 "detritívoro", "depredador", "herbívoro", "detritívoro", "detritívoro", 
                                                                                 "herbívoro", "detritívoro", "detritívoro")), class = "data.frame", row.names = c("Andesiops", 
                                                                                                                                                                  "Meridialaris", "Polycentropus", "Austrelmis", "Prionocyphon", 
                                                                                                                                                                  "Neoplasta", "Gigantodax", "Simulium", "Tipula", "Alotanypus", 
                                                                                                                                                                  "Pentaneura", "Corynoneura", "Cricotopus", "Tanytarsus", "Podonomus", 
                                                                                                                                                                  "Podonomopsis", "Parochlus"))```

dromano · March 4, 2020, 8:09pm

Still cutting it off. How about you try running these commands, one at a time:

sink('dput_output.txt')
dput(chi)
sink()

This will send the output of the dput() command to a file called 'dput_output.txt', which you can then open, copy, and paste here. Could you try that?

Manu2592 · March 4, 2020, 8:25pm

structure(list(Taxon = c("Andesiops", "Meridialaris", "Polycentropus",
"Austrelmis", "Prionocyphon", "Neoplasta", "Gigantodax", "Simulium",
"Tipula", "Alotanypus", "Pentaneura", "Corynoneura", "Cricotopus",
"Tanytarsus", "Podonomus", "Podonomopsis", "Parochlus"), MOPF = c(75,
5, 20, 93, 40, 98, 65, 30, 30, 60, 35, 15, 90, 95, 25, 85, 95
), MA = c(25, 95, 0, 7, 0, 2, 15, 65, 0, 20, 5, 85, 10, 5, 75,
15, 5), RA = c(0, 0, 80, 0, 60, 0, 20, 5, 0, 20, 60, 0, 0, 0,
0, 0, 0), TV = c(0, 0, 0, 0, 0, 0, 0, 0, 70, 0, 0, 0, 0, 0, 0,
0, 0), GT = c("detritívoro", "herbívoro", "depredador", "detritívoro",
"depredador", "detritívoro", "detritívoro", "herbívoro", "herbívoro",
"detritívoro", "depredador", "herbívoro", "detritívoro", "detritívoro",
"herbívoro", "detritívoro", "detritívoro")), class = "data.frame", row.names = c("Andesiops",
"Meridialaris", "Polycentropus", "Austrelmis", "Prionocyphon",
"Neoplasta", "Gigantodax", "Simulium", "Tipula", "Alotanypus",
"Pentaneura", "Corynoneura", "Cricotopus", "Tanytarsus", "Podonomus",
"Podonomopsis", "Parochlus"))

dromano · March 4, 2020, 11:23pm

This works, but in general you should place the output between a pair of triple backticks, like this:

```
[paste output of dput(chi) here]
```

One thing that confuses me is that if you apply prcomp() to this table, you don't get PCA coordinates for individual taxa; you get them for each of the numeric columns of chi -- how did you get taxon coordinates to make your plot?