error in `compute_aesthetics()`: ! Aesthetics are not valid data columns.

Vnaitnle · April 26, 2024, 12:44pm

Hello, i'm struggling with an error on R. I'm trying to get a plot that display the significativity like this
Sans titre

My code is here:
stat.test <- datanett %>% t_test(willingness ~ environment, p.adjust.method = "bonferroni")
stat.test
stat.test <- stat.test %>%
add_xy_position(fun="mean",x="environment")

g2 <- datanett %>%
ggplot(aes(x=environment, y=willingness, color=environment)) +
geom_violin(width=1,
alpha=0.2) +
geom_point(stat="summary",
fun="mean",
size=5) +
geom_boxplot(width=0.1,
color="black",
alpha=0.3) +
scale_color_manual(values=met.brewer("Tiepolo"))+
labs(x="Environnement",
y="Willingness to cross")+
theme_minimal() +
theme(legend.position="none",
axis.title = element_text(size = 15),
axis.text = element_text( size = 15))
g2 + stat_pvalue_manual(stat.test, label = "p", tip.length = 0.01)

This print this error

Error:
! Problem while computing aesthetics.
Error occurred in the 4th layer.
Caused by error in compute_aesthetics():
! Aesthetics are not valid data columns.
The following aesthetics are invalid:
fill = environment
Did you mistype the name of a data column or forget to add
after_stat()?

When I remove fill="environment" in the aes function i don't have anymore this error but i have a ugly plot without color. Do you have clue to help me having my beautiful plot?
Thank you

jrkrideau · April 26, 2024, 1:00pm

What packages do you have loaded?

Can you supply us with some sample data? A handy way to supply some sample data is the dput() function. In the case of a large dataset something like dput(head(mydata, 100)) should supply the data we need. Just do dput(mydata) where mydata is your data. Copy the output and paste it here between
```

```

Vnaitnle · April 26, 2024, 1:35pm

Thank you for your answer, I use these packages: ggplot2, rstatix, tydiverse, dplyr, ggpubr, MetBrewer

I'm not sure they are all usefull for this part.
Here are my data

structure(list(id = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L), levels = c("1", 
"2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", 
"14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", 
"25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", 
"36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", 
"47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", 
"58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", 
"69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", 
"80", "81", "82", "83", "84"), class = "factor"), duree = c(118, 
118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 
118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 150, 150, 150, 
150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 
150, 150, 150, 150, 150, 150, 150, 150, 186, 186, 186, 186, 186, 
186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 
186, 186, 186, 186, 186, 186, 492, 492, 492, 492, 492, 492, 492, 
492, 492, 492, 492, 492, 492, 492, 492, 492, 492, 492, 492, 492, 
492, 492, 492, 492, 204, 204, 204, 204), gender = c("Woman", 
"Woman", "Woman", "Woman", "Woman", "Woman", "Woman", "Woman", 
"Woman", "Woman", "Woman", "Woman", "Woman", "Woman", "Woman", 
"Woman", "Woman", "Woman", "Woman", "Woman", "Woman", "Woman", 
"Woman", "Woman", "Woman", "Woman", "Woman", "Woman", "Woman", 
"Woman", "Woman", "Woman", "Woman", "Woman", "Woman", "Woman", 
"Woman", "Woman", "Woman", "Woman", "Woman", "Woman", "Woman", 
"Woman", "Woman", "Woman", "Woman", "Woman", "Man", "Man", "Man", 
"Man", "Man", "Man", "Man", "Man", "Man", "Man", "Man", "Man", 
"Man", "Man", "Man", "Man", "Man", "Man", "Man", "Man", "Man", 
"Man", "Man", "Man", "Woman", "Woman", "Woman", "Woman", "Woman", 
"Woman", "Woman", "Woman", "Woman", "Woman", "Woman", "Woman", 
"Woman", "Woman", "Woman", "Woman", "Woman", "Woman", "Woman", 
"Woman", "Woman", "Woman", "Woman", "Woman", "Woman", "Woman", 
"Woman", "Woman"), age = c(22, 22, 22, 22, 22, 22, 22, 22, 22, 
22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 21, 
21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 
21, 21, 21, 21, 21, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 
45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 21, 
21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 
21, 21, 21, 21, 21, 21, 21, 24, 24, 24, 24), eHMI = structure(c(2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 
2L, 2L, 2L), levels = c("Absent", "Can cross", "Can not cross"
), class = "factor"), environment = structure(c(2L, 2L, 2L, 2L, 
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L
), levels = c("Accompanied", "Alone"), class = "factor"), distance = structure(c(1L, 
1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 
1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 
1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 
1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 
1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 
1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 
1L, 2L, 2L), levels = c("10m", "30m"), class = "factor"), speed = structure(c(2L, 
1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 
1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 
1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 
1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 
1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 
1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 
1L, 2L, 1L), levels = c("15km/h", "7km/h"), class = "factor"), 
    willingness = c(10, 10, 10, 10, 11, 11, 11, NA, 11, 11, 10, 
    10, 11, 10, 10, 14, 10, 13, 10, 10, 10, 12, 10, 12, 9, 10, 
    9, 9, 8, 8, 8, 8, 8, 9, 10, 8, 9, 9, 9, 8, 10, 9, 9, 9, 10, 
    10, NA, 10, 10, 9, 8, 9, 9, 9, 9, 9, 9, 8, 9, 9, 9, 8, 8, 
    9, 8, 9, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 
    0, 0, 0, 0, 0, 0, 0, 0, 14, 6, 20, 20, 18, 4, 20, 20, 17, 
    16, 16, 16), cluster = structure(c(3L, 3L, 3L, 3L, 3L, 3L, 
    3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
    3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
    4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
    4L, 4L, 4L, 4L), levels = c("1", "2", "3", "4"), class = "factor"), 
    all = c("Can cross-Alone-10m-7km/h", "Can cross-Alone-10m-15km/h", 
    "Can cross-Alone-30m-7km/h", "Can cross-Alone-30m-15km/h", 
    "Can cross-Accompanied-10m-7km/h", "Can cross-Accompanied-10m-15km/h", 
    "Can cross-Accompanied-30m-7km/h", "Can cross-Accompanied-10m-15km/h", 
    "Can not cross-Alone-10m-7km/h", "Can not cross-Alone-10m-7km/h", 
    "Can not cross-Alone-30m-15km/h", "Can not cross-Alone-30m-15km/h", 
    "Can not cross-Accompanied-10m-7km/h", "Can not cross-Accompanied-10m-15km/h", 
    "Can not cross-Accompanied-30m-7km/h", "Can not cross-Accompanied-30m-15km/h", 
    "Absent-Alone-10m-7km/h", "Absent-Alone-10m-15km/h", "Absent-Alone-30m-7km/h", 
    "Absent-Alone-30m-15km/h", "Absent-Accompanied-10m-7km/h", 
    "Absent-Accompanied-10m-15km/h", "Absent-Accompanied-30m-7km/h", 
    "Absent-Accompanied-30m-15km/h", "Can cross-Alone-10m-7km/h", 
    "Can cross-Alone-10m-15km/h", "Can cross-Alone-30m-7km/h", 
    "Can cross-Alone-30m-15km/h", "Can cross-Accompanied-10m-7km/h", 
    "Can cross-Accompanied-10m-15km/h", "Can cross-Accompanied-30m-7km/h", 
    "Can cross-Accompanied-10m-15km/h", "Can not cross-Alone-10m-7km/h", 
    "Can not cross-Alone-10m-7km/h", "Can not cross-Alone-30m-15km/h", 
    "Can not cross-Alone-30m-15km/h", "Can not cross-Accompanied-10m-7km/h", 
    "Can not cross-Accompanied-10m-15km/h", "Can not cross-Accompanied-30m-7km/h", 
    "Can not cross-Accompanied-30m-15km/h", "Absent-Alone-10m-7km/h", 
    "Absent-Alone-10m-15km/h", "Absent-Alone-30m-7km/h", "Absent-Alone-30m-15km/h", 
    "Absent-Accompanied-10m-7km/h", "Absent-Accompanied-10m-15km/h", 
    "Absent-Accompanied-30m-7km/h", "Absent-Accompanied-30m-15km/h", 
    "Can cross-Alone-10m-7km/h", "Can cross-Alone-10m-15km/h", 
    "Can cross-Alone-30m-7km/h", "Can cross-Alone-30m-15km/h", 
    "Can cross-Accompanied-10m-7km/h", "Can cross-Accompanied-10m-15km/h", 
    "Can cross-Accompanied-30m-7km/h", "Can cross-Accompanied-10m-15km/h", 
    "Can not cross-Alone-10m-7km/h", "Can not cross-Alone-10m-7km/h", 
    "Can not cross-Alone-30m-15km/h", "Can not cross-Alone-30m-15km/h", 
    "Can not cross-Accompanied-10m-7km/h", "Can not cross-Accompanied-10m-15km/h", 
    "Can not cross-Accompanied-30m-7km/h", "Can not cross-Accompanied-30m-15km/h", 
    "Absent-Alone-10m-7km/h", "Absent-Alone-10m-15km/h", "Absent-Alone-30m-7km/h", 
    "Absent-Alone-30m-15km/h", "Absent-Accompanied-10m-7km/h", 
    "Absent-Accompanied-10m-15km/h", "Absent-Accompanied-30m-7km/h", 
    "Absent-Accompanied-30m-15km/h", "Can cross-Alone-10m-7km/h", 
    "Can cross-Alone-10m-15km/h", "Can cross-Alone-30m-7km/h", 
    "Can cross-Alone-30m-15km/h", "Can cross-Accompanied-10m-7km/h", 
    "Can cross-Accompanied-10m-15km/h", "Can cross-Accompanied-30m-7km/h", 
    "Can cross-Accompanied-10m-15km/h", "Can not cross-Alone-10m-7km/h", 
    "Can not cross-Alone-10m-7km/h", "Can not cross-Alone-30m-15km/h", 
    "Can not cross-Alone-30m-15km/h", "Can not cross-Accompanied-10m-7km/h", 
    "Can not cross-Accompanied-10m-15km/h", "Can not cross-Accompanied-30m-7km/h", 
    "Can not cross-Accompanied-30m-15km/h", "Absent-Alone-10m-7km/h", 
    "Absent-Alone-10m-15km/h", "Absent-Alone-30m-7km/h", "Absent-Alone-30m-15km/h", 
    "Absent-Accompanied-10m-7km/h", "Absent-Accompanied-10m-15km/h", 
    "Absent-Accompanied-30m-7km/h", "Absent-Accompanied-30m-15km/h", 
    "Can cross-Alone-10m-7km/h", "Can cross-Alone-10m-15km/h", 
    "Can cross-Alone-30m-7km/h", "Can cross-Alone-30m-15km/h"
    ), allcode = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 
    9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 
    21L, 22L, 23L, 24L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 
    11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 
    23L, 24L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 
    13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 
    1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 
    15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 1L, 2L, 
    3L, 4L), levels = c("0000", "0001", "0010", "0011", "0100", 
    "0101", "0110", "0111", "1000", "1001", "1010", "1011", "1100", 
    "1101", "1110", "1111", "2000", "2001", "2010", "2011", "2100", 
    "2101", "2110", "2111"), class = "factor"), ido = c(1, 2, 
    3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 
    19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 
    34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 
    49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 
    64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 
    79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 
    94, 95, 96, 97, 98, 99, 100)), row.names = c(NA, -100L), class = c("tbl_df", 
"tbl", "data.frame"))

jrkrideau · April 26, 2024, 1:42pm

Thanks, the data came through nicely. It is always useful to know what packages are being used. It this case it was clear that you were using an adaption of ggplot2 but I could not remember what it was.

jrkrideau · April 26, 2024, 2:40pm

Can you give us your complete code? It is difficult to see what you are doing without the rest of what you are doing.

For some general information on asking questions on the form see FAQ Asking Questions

jrkrideau · April 26, 2024, 3:19pm

I don't think I need anything more.

Everything seems to be working fine for me.

library(tidyverse)
library(ggpubr) 
library(rstatix)
library(MetBrewer)

DT <- read.csv('raw.data.csv')

stat.test <- DT %>% t_test(willingness ~ environment, p.adjust.method = "bonferroni")

stat.test <- stat.test %>%
add_xy_position(fun="mean",x="environment")

g2 <- DT %>%
ggplot(aes(x=environment, y=willingness, color=environment)) +
geom_violin(width=1,
alpha=0.2) +
geom_point(stat="summary",
fun="mean",
size=5) +
geom_boxplot(width=0.1,
color="black",
alpha=0.3) +
scale_color_manual(values=met.brewer("Tiepolo"))+
labs(x="Environnement",
y="Willingness to cross")+
theme_minimal() +
theme(legend.position="none",
axis.title = element_text(size = 15),
axis.text = element_text( size = 15))

g2 + stat_pvalue_manual(stat.test, label = "p", tip.length = 0.01)

Vnaitnle · May 3, 2024, 4:21pm

Sorry for the response time. I put the wrong code. The problem is in the aes function when i add a fill argument.

This gives me an aes function like this:

ggplot(aes(x=environment, y=willingness, color=environment, fill=environment))

When i do this, R print me the error message written above.

jrkrideau · May 3, 2024, 7:23pm

I think the problem is that the *fill = * command does not work with geom_point() . You can set the colour but not the fill.

dromano · May 5, 2024, 2:34pm

It does, but not with the default points. Not sure the OP intended to use anything besides the default points, though.

jrkrideau · May 5, 2024, 3:25pm

I was wondering about that after I replied. Does one of the ggXXX packages supply this option?

dromano · May 5, 2024, 4:05pm

It's part of ggplot2 itself, but it depends on the shape of the point. Here's a link to the shape section of the vignette on aesthetics:

jrkrideau · May 5, 2024, 4:13pm

Thanks. I was looking for a "fill" command a few months ago and missed this completely. I think I just assumed from the help that one could not do it