Object missing or new axis labels made using ggpubr::stat_pvalue_manual on violin plot with fill aspect
I have ran into a problem with using ggpubr::stat_pvalue_manual with a ggplot2 violin plot that has a fill aspect. There is either an issue of the fill aspect group not being found as an object or the brackets are misaligned completely. To start off I have easily made a violin/boxplot plot with the pairwise brackets using ggplot, but before that I make the table of adjusted p values from the contrasts of my estimated marginal means. More information about estimated marginal means can be found in emmeans package. Below is an example of what I would like the plot to look like without the fill aspect.
## make table of adjusted p values
stat.test <- tibble::tribble(
~group1, ~group2, ~p.adj,
"Non-brooding", "Brooding_wo_embryos", 1.0000,
"Non-brooding", "Brooding_w_embryos", 0.0001,
"Brooding_wo_embryos", "Brooding_w_embryos", 0.0001)
## test figure for stackoverflow
library(ggplot2)
ggplot(x, aes(x=Reproductive, y=Total_Phosphorus)) +
geom_violin(width = 1, size = 1) +
geom_boxplot(position = position_dodge(width = 1), width = 0.1, color="black", alpha=0.5, size = 1) +
## pairwise comparisons added here
stat_pvalue_manual(stat.test, y.position = 0.00125, step.increase = 0.2, label = "p.adj")
I get the expected outcome: 
Now I would like to do the same with a plot that has a fill aspect but R keeps telling me that I P_treatment is not an object, but I believe that P_treatment is an object since dataframe$P_treatment returns the item.
First attempted adjusted p value table does not work:
stat.test2 <- tibble::tribble(
~group1, ~group2, ~p.adj,
"Intermediate Non-brooding", "Low Non-brooding", 0.6991,
"Intermediate Non-brooding", "Intermediate Brooding_wo_embryos", 1.0000,
"Intermediate Non-brooding", "Low Brooding_wo_embryos", 1.0000,
"Intermediate Non-brooding", "Intermediate Brooding_w_embryos", 0.0001,
"Intermediate Non-brooding", "Low Brooding_w_embryos", 0.0001,
"Low Non-brooding", "Intermediate Brooding_wo_embryos", 1.0000,
"Low Non-brooding", "Low Brooding_wo_embryos", 1.0000,
"Low Non-brooding", "Intermediate Brooding_w_embryos", 0.0001,
"Low Non-brooding", "Low Brooding_w_embryos", 0.0001,
"Intermediate Brooding_wo_embryos", "Low Brooding_wo_embryos", 1.0000,
"Intermediate Brooding_wo_embryos", "Intermediate Brooding_w_embryos", 0.0001,
"Intermediate Brooding_wo_embryos", "Low Brooding_w_embryos", 0.0001,
"Low Brooding_wo_embryos", "Intermediate Brooding_w_embryos", 0.0001,
"Low Brooding_wo_embryos", "Low Brooding_w_embryos", 0.0001,
"Intermediate Brooding_w_embryos", "Low Brooding_w_embryos", 1.0000)
## test figure for stack overflow
library(ggplot2)
ggplot(x, aes(x=Reproductive, y=Total_Phosphorus, shape = P_treatment)) +
geom_violin(width = 1) +
geom_boxplot(position = position_dodge(width = 1), width = 0.1, color="black", alpha=0.5) +
stat_pvalue_manual(stat.test2, y.position = 0.00125, step.increase = 0.1, label = "p.adj")
Error:
! Problem while computing aesthetics.
ℹ Error occurred in the 3rd layer.
Caused by error:
! object 'P_treatment' not found
Run rlang::last_trace() to see where the error occurred.
I tried this method again, but I define P_treatment. I know I did not define P_treatment in the table of p values correctly, but this is just a test. Now, the issue is my brackets are attached to vectors that aren't real and all the way to the right.
Second attempted adjusted p value table does not work:
stat.test2 <- tibble::tribble(
~P_treatment, ~group1, ~group2, ~p.adj,
"Intermediate", "Intermediate Non-brooding", "Low Non-brooding", 0.6991,
"Intermediate", "Intermediate Non-brooding", "Intermediate Brooding_wo_embryos", 1.0000,
"Intermediate", "Intermediate Non-brooding", "Low Brooding_wo_embryos", 1.0000,
"Intermediate", "Intermediate Non-brooding", "Intermediate Brooding_w_embryos", 0.0001,
"Intermediate", "Intermediate Non-brooding", "Low Brooding_w_embryos", 0.0001,
"Intermediate", "Low Non-brooding", "Intermediate Brooding_wo_embryos", 1.0000,
"Intermediate", "Low Non-brooding", "Low Brooding_wo_embryos", 1.0000,
"Intermediate", "Low Non-brooding", "Intermediate Brooding_w_embryos", 0.0001,
"Intermediate", "Low Non-brooding", "Low Brooding_w_embryos", 0.0001,
"Intermediate", "Intermediate Brooding_wo_embryos", "Low Brooding_wo_embryos", 1.0000,
"Intermediate", "Intermediate Brooding_wo_embryos", "Intermediate Brooding_w_embryos", 0.0001,
"Intermediate", "Intermediate Brooding_wo_embryos", "Low Brooding_w_embryos", 0.0001,
"Intermediate", "Low Brooding_wo_embryos", "Intermediate Brooding_w_embryos", 0.0001,
"Intermediate", "Low Brooding_wo_embryos", "Low Brooding_w_embryos", 0.0001,
"Intermediate", "Intermediate Brooding_w_embryos", "Low Brooding_w_embryos", 1.0000)
library(ggplot2)
ggplot(x, aes(x=Reproductive, y=Total_Phosphorus, shape = P_treatment)) +
geom_violin(width = 1) +
geom_boxplot(position = position_dodge(width = 1), width = 0.1, color="black", alpha=0.5) +
stat_pvalue_manual(stat.test2, y.position = 0.00125, step.increase = 0.1, label = "p.adj")
Third attempted adjusted p value table does not work:
stat.test2 <- tibble::tribble(
~Reproductive, ~P_treatment, ~group1, ~group2, ~p.adj,
"Non-brooding", "Intermediate", "Intermediate Non-brooding", "Low Non-brooding", 0.6991,
"Non-brooding", "Intermediate", "Intermediate Non-brooding", "Intermediate Brooding_wo_embryos", 1.0000,
"Non-brooding", "Intermediate", "Intermediate Non-brooding", "Low Brooding_wo_embryos", 1.0000,
"Non-brooding", "Intermediate", "Intermediate Non-brooding", "Intermediate Brooding_w_embryos", 0.0001,
"Non-brooding", "Intermediate", "Intermediate Non-brooding", "Low Brooding_w_embryos", 0.0001,
"Non-brooding", "Intermediate", "Low Non-brooding", "Intermediate Brooding_wo_embryos", 1.0000,
"Non-brooding", "Intermediate", "Low Non-brooding", "Low Brooding_wo_embryos", 1.0000,
"Non-brooding", "Intermediate", "Low Non-brooding", "Intermediate Brooding_w_embryos", 0.0001,
"Non-brooding", "Intermediate", "Low Non-brooding", "Low Brooding_w_embryos", 0.0001,
"Non-brooding", "Intermediate", "Intermediate Brooding_wo_embryos", "Low Brooding_wo_embryos", 1.0000,
"Non-brooding", "Intermediate", "Intermediate Brooding_wo_embryos", "Intermediate Brooding_w_embryos", 0.0001,
"Non-brooding", "Intermediate", "Intermediate Brooding_wo_embryos", "Low Brooding_w_embryos", 0.0001,
"Non-brooding", "Intermediate", "Low Brooding_wo_embryos", "Intermediate Brooding_w_embryos", 0.0001,
"Non-brooding", "Intermediate", "Low Brooding_wo_embryos", "Low Brooding_w_embryos", 0.0001,
"Non-brooding", "Intermediate", "Intermediate Brooding_w_embryos", "Low Brooding_w_embryos", 1.0000)
## test figure for stack overflow
library(ggplot2)
ggplot(x, aes(x=Reproductive, y=Total_Phosphorus, shape = P_treatment)) +
geom_violin(width = 1) +
geom_boxplot(position = position_dodge(width = 1), width = 0.1, color="black", alpha=0.5) +
stat_pvalue_manual(stat.test2, y.position = 0.00125, step.increase = 0.1, label = "p.adj")
Here is when I noticed that my table makes new groups out of my data. However, my data is not structured as a mix P_treatment and Reproductive - they are separate columns. You might have to click on this image as it is very blurry!
My data:
A tibble: 209 × 3
P_treatment Reproductive Total_Phosphorus
<fct> <fct> <dbl>
1 Low Non-brooding 0.000321
2 Intermediate Brooding_w_embryos 0.000733
3 Intermediate Brooding_wo_embryos 0.000341
4 Low Brooding_w_embryos 0.00101
5 Low Brooding_wo_embryos 0.000410
6 Intermediate Non-brooding 0.000497
7 Intermediate Brooding_w_embryos 0.000697
8 Intermediate Brooding_wo_embryos 0.000415
9 Low Brooding_w_embryos 0.000491
10 Low Brooding_w_embryos 0.000863
11 Low Brooding_wo_embryos 0.000273
12 Low Brooding_wo_embryos 0.000365
13 Low Non-brooding 0.000556
14 Low Non-brooding 0.000317
15 Intermediate Brooding_w_embryos 0.000804
16 Intermediate Brooding_wo_embryos 0.000498
17 Low Brooding_w_embryos 0.000708
18 Low Brooding_wo_embryos 0.000402
19 Low Brooding_wo_embryos 0.000398
20 Low Brooding_w_embryos 0.000628
21 Low Brooding_wo_embryos 0.000315
22 Low Non-brooding 0.000619
23 Intermediate Brooding_w_embryos 0.000674
24 Intermediate Brooding_wo_embryos 0.000276
25 Intermediate Brooding_w_embryos 0.000899
26 Intermediate Brooding_wo_embryos 0.000420
27 Intermediate Non-brooding 0.000468
28 Low Brooding_w_embryos 0.000715
29 Low Brooding_w_embryos 0.000842
30 Low Brooding_wo_embryos 0.000443
31 Low Brooding_wo_embryos 0.000517
32 Low Brooding_w_embryos 0.000843
33 Low Brooding_wo_embryos 0.000589
34 Low Brooding_w_embryos 0.00100
35 Low Brooding_wo_embryos 0.000470
36 Intermediate Brooding_w_embryos 0.000573
37 Intermediate Brooding_w_embryos 0.000785
38 Intermediate Brooding_wo_embryos 0.000162
39 Intermediate Brooding_wo_embryos 0.000507
40 Low Non-brooding 0.000249
41 Intermediate Brooding_w_embryos 0.00078
42 Intermediate Brooding_wo_embryos 0.000450
43 Low Non-brooding 0.000327
44 Low Non-brooding 0.000322
45 Low Brooding_w_embryos 0.00091
46 Low Brooding_wo_embryos 0.000480
47 Intermediate Brooding_w_embryos 0.000954
48 Intermediate Brooding_wo_embryos 0.000472
49 Intermediate Non-brooding 0.000461
50 Low Brooding_w_embryos 0.00024
51 Low Brooding_w_embryos 0.000749
52 Low Brooding_w_embryos 0.000713
53 Low Brooding_wo_embryos 0.000122
54 Low Brooding_wo_embryos 0.000336
55 Low Brooding_wo_embryos 0.000419
56 Low Non-brooding 0.000319
57 Low Non-brooding 0.000301
58 Intermediate Non-brooding 0.000341
59 Low Non-brooding 0.000733
60 Intermediate Brooding_w_embryos 0.000688
61 Intermediate Brooding_w_embryos 0.000828
62 Intermediate Brooding_wo_embryos 0.0000546
63 Intermediate Brooding_wo_embryos 0.000341
64 Intermediate Non-brooding 0.000501
65 Intermediate Non-brooding 0.000367
66 Low Brooding_w_embryos 0.00078
67 Low Brooding_wo_embryos 0.000522
68 Low Non-brooding 0.000560
69 Intermediate Brooding_wo_embryos 0.000329
70 Intermediate Non-brooding 0.000340
71 Intermediate Non-brooding 0.000438
72 Intermediate Non-brooding 0.000304
73 Low Non-brooding 0.000291
74 Low Brooding_wo_embryos 0.000507
75 Low Non-brooding 0.000462
76 Intermediate Non-brooding 0.000127
77 Intermediate Brooding_w_embryos 0.000804
78 Intermediate Brooding_w_embryos 0.000446
79 Intermediate Brooding_w_embryos 0.000747
80 Intermediate Brooding_wo_embryos 0.000297
81 Intermediate Brooding_wo_embryos 0.000308
82 Intermediate Brooding_wo_embryos 0.000348
83 Low Non-brooding 0.000500
84 Low Brooding_wo_embryos 0.000512
85 Intermediate Brooding_w_embryos 0.000822
86 Intermediate Brooding_w_embryos 0.00108
87 Intermediate Brooding_wo_embryos 0.000436
88 Intermediate Brooding_wo_embryos 0.000560
89 Intermediate Brooding_w_embryos 0.000871
90 Intermediate Brooding_wo_embryos 0.000265
91 Low Brooding_w_embryos 0.000485
92 Low Brooding_wo_embryos 0.000241
93 Low Non-brooding 0.000608
94 Low Non-brooding 0.000233
95 Low Non-brooding 0.000481
96 Low Brooding_w_embryos 0.00106
97 Low Brooding_wo_embryos 0.000596
98 Intermediate Non-brooding 0.000254
99 Low Non-brooding 0.000596
100 Low Non-brooding 0.000481
101 Low Brooding_w_embryos 0.000588
102 Low Brooding_w_embryos 0.000574
103 Low Brooding_w_embryos 0.00132
104 Low Brooding_wo_embryos 0.0000973
105 Low Brooding_wo_embryos 0.000281
106 Low Brooding_wo_embryos 0.000291
107 Low Non-brooding 0.000265
108 Low Non-brooding 0.000158
109 Intermediate Brooding_w_embryos 0.00107
110 Intermediate Brooding_w_embryos 0.000415
111 Intermediate Brooding_w_embryos 0.000686
112 Intermediate Brooding_w_embryos 0.000583
113 Intermediate Brooding_w_embryos 0.000852
114 Intermediate Brooding_wo_embryos 0.000565
115 Intermediate Brooding_wo_embryos 0.000137
116 Intermediate Brooding_wo_embryos 0.000314
117 Intermediate Brooding_wo_embryos 0.000295
118 Intermediate Brooding_wo_embryos 0.000355
119 Intermediate Non-brooding 0.000347
120 Intermediate Non-brooding 0.000676
121 Intermediate Non-brooding 0.000347
122 Low Brooding_w_embryos 0.000682
123 Low Brooding_wo_embryos 0.000298
124 Low Non-brooding 0.000639
125 Low Non-brooding 0.000368
126 Intermediate Brooding_w_embryos 0.000974
127 Intermediate Brooding_wo_embryos 0.000460
128 Intermediate Non-brooding 0.000340
129 Intermediate Brooding_w_embryos 0.0006
130 Intermediate Brooding_w_embryos 0.000706
131 Intermediate Brooding_wo_embryos 0.000351
132 Intermediate Brooding_wo_embryos 0.000300
133 Intermediate Non-brooding 0.000382
134 Low Brooding_wo_embryos 0.000422
135 Low Non-brooding 0.000405
136 Low Non-brooding 0.000300
137 Low Brooding_w_embryos 0.000839
138 Low Brooding_wo_embryos 0.000580
139 Intermediate Brooding_w_embryos 0.0007
140 Intermediate Brooding_wo_embryos 0.000241
141 Intermediate Non-brooding 0.000413
142 Intermediate Non-brooding 0.0000462
143 Low Brooding_w_embryos 0.00106
144 Low Brooding_wo_embryos 0.000408
145 Low Non-brooding 0.000239
146 Low Non-brooding 0.000416
147 Low Non-brooding 0.000330
148 Low Non-brooding 0.000365
149 Intermediate Non-brooding 0.000317
150 Low Non-brooding 0.000414
151 Low Non-brooding 0.000434
152 Intermediate Non-brooding 0.0000394
153 Intermediate Brooding_w_embryos 0.000722
154 Intermediate Brooding_wo_embryos 0.000299
155 Low Brooding_w_embryos 0.00104
156 Low Brooding_wo_embryos 0.000404
157 Low Non-brooding 0.000238
158 Intermediate Brooding_w_embryos 0.000757
159 Intermediate Brooding_w_embryos 0.000991
160 Intermediate Brooding_wo_embryos 0.000304
161 Intermediate Brooding_wo_embryos 0.000332
162 Intermediate Non-brooding 0.000239
163 Intermediate Non-brooding 0.000494
164 Intermediate Non-brooding 0.000269
165 Low Brooding_w_embryos 0.000839
166 Low Brooding_wo_embryos 0.000392
167 Low Non-brooding 0.000433
168 Low Non-brooding 0.000506
169 Intermediate Non-brooding 0.000449
170 Intermediate Non-brooding 0.000180
171 Low Non-brooding 0.000406
172 Intermediate Brooding_w_embryos 0.000944
173 Intermediate Brooding_w_embryos 0.000602
174 Intermediate Brooding_wo_embryos 0.000452
175 Intermediate Brooding_wo_embryos 0.000331
176 Intermediate Non-brooding 0.000260
177 Low Non-brooding 0.000299
178 Intermediate Brooding_w_embryos 0.000797
179 Intermediate Brooding_w_embryos 0.000619
180 Intermediate Brooding_wo_embryos 0.000391
181 Intermediate Brooding_wo_embryos 0.000358
182 Low Non-brooding 0.000640
183 Intermediate Brooding_w_embryos 0.000799
184 Intermediate Brooding_wo_embryos 0.000340
185 Low Brooding_w_embryos 0.000779
186 Low Brooding_w_embryos 0.000769
187 Low Brooding_wo_embryos 0.000304
188 Low Brooding_wo_embryos 0.000450
189 Intermediate Brooding_w_embryos 0.000609
190 Intermediate Brooding_wo_embryos 0.000376
191 Intermediate Non-brooding 0.000313
192 Low Brooding_wo_embryos 0.000456
193 Intermediate Brooding_w_embryos 0.000751
194 Intermediate Brooding_w_embryos 0.000453
195 Intermediate Brooding_wo_embryos 0.000378
196 Intermediate Brooding_wo_embryos 0.000200
197 Intermediate Brooding_w_embryos 0.000563
198 Intermediate Brooding_wo_embryos 0.000342
199 Low Non-brooding 0.000485
200 Intermediate Brooding_w_embryos 0.00109
201 Intermediate Brooding_wo_embryos 0.000567
202 Low Brooding_w_embryos 0.00096
203 Low Brooding_wo_embryos 0.000598
204 Intermediate Brooding_w_embryos 0.00063
205 Intermediate Brooding_wo_embryos 0.000408
206 Low Brooding_w_embryos 0.00133
207 Low Brooding_wo_embryos 0.000517
208 Intermediate Brooding_w_embryos 0.00108
209 Intermediate Brooding_wo_embryos 0.000557
I would like to note here that dataframe$P_treatment has 2 levels and dataframe$Reproductive has 3 levels. I know that all groups are not in one P_treatment or Reproductive mode level, but I tried using one variation of the group as a test and there still was no difference between second and third attempt.
This method has worked before with no fill so I am confused as to it will not work now. Thank you very much!
Solution
You have factor levels in your dataframe "x" (e.g. "Non-brooding") that aren't in "stat.test2" ("Low Non-brooding"). If you create the equivalent factor levels (using e.g. interaction() ) ggplot2 doesn't return the error, e.g.
Load libraries and data:
library(tidyverse)
library(ggpubr)
df <- read.table(text = "rn P_treatment Reproductive Total_Phosphorus
1 Low Non-brooding 0.000321
2 Intermediate Brooding_w_embryos 0.000733
3 Intermediate Brooding_wo_embryos 0.000341
4 Low Brooding_w_embryos 0.00101
5 Low Brooding_wo_embryos 0.000410
6 Intermediate Non-brooding 0.000497
7 Intermediate Brooding_w_embryos 0.000697
8 Intermediate Brooding_wo_embryos 0.000415
9 Low Brooding_w_embryos 0.000491
10 Low Brooding_w_embryos 0.000863
11 Low Brooding_wo_embryos 0.000273
12 Low Brooding_wo_embryos 0.000365
13 Low Non-brooding 0.000556
14 Low Non-brooding 0.000317
15 Intermediate Brooding_w_embryos 0.000804
16 Intermediate Brooding_wo_embryos 0.000498
17 Low Brooding_w_embryos 0.000708
18 Low Brooding_wo_embryos 0.000402
19 Low Brooding_wo_embryos 0.000398
20 Low Brooding_w_embryos 0.000628
21 Low Brooding_wo_embryos 0.000315
22 Low Non-brooding 0.000619
23 Intermediate Brooding_w_embryos 0.000674
24 Intermediate Brooding_wo_embryos 0.000276
25 Intermediate Brooding_w_embryos 0.000899
26 Intermediate Brooding_wo_embryos 0.000420
27 Intermediate Non-brooding 0.000468
28 Low Brooding_w_embryos 0.000715
29 Low Brooding_w_embryos 0.000842
30 Low Brooding_wo_embryos 0.000443
31 Low Brooding_wo_embryos 0.000517
32 Low Brooding_w_embryos 0.000843
33 Low Brooding_wo_embryos 0.000589
34 Low Brooding_w_embryos 0.00100
35 Low Brooding_wo_embryos 0.000470
36 Intermediate Brooding_w_embryos 0.000573
37 Intermediate Brooding_w_embryos 0.000785
38 Intermediate Brooding_wo_embryos 0.000162
39 Intermediate Brooding_wo_embryos 0.000507
40 Low Non-brooding 0.000249
41 Intermediate Brooding_w_embryos 0.00078
42 Intermediate Brooding_wo_embryos 0.000450
43 Low Non-brooding 0.000327
44 Low Non-brooding 0.000322
45 Low Brooding_w_embryos 0.00091
46 Low Brooding_wo_embryos 0.000480
47 Intermediate Brooding_w_embryos 0.000954
48 Intermediate Brooding_wo_embryos 0.000472
49 Intermediate Non-brooding 0.000461
50 Low Brooding_w_embryos 0.00024
51 Low Brooding_w_embryos 0.000749
52 Low Brooding_w_embryos 0.000713
53 Low Brooding_wo_embryos 0.000122
54 Low Brooding_wo_embryos 0.000336
55 Low Brooding_wo_embryos 0.000419
56 Low Non-brooding 0.000319
57 Low Non-brooding 0.000301
58 Intermediate Non-brooding 0.000341
59 Low Non-brooding 0.000733
60 Intermediate Brooding_w_embryos 0.000688
61 Intermediate Brooding_w_embryos 0.000828
62 Intermediate Brooding_wo_embryos 0.0000546
63 Intermediate Brooding_wo_embryos 0.000341
64 Intermediate Non-brooding 0.000501
65 Intermediate Non-brooding 0.000367
66 Low Brooding_w_embryos 0.00078
67 Low Brooding_wo_embryos 0.000522
68 Low Non-brooding 0.000560
69 Intermediate Brooding_wo_embryos 0.000329
70 Intermediate Non-brooding 0.000340
71 Intermediate Non-brooding 0.000438
72 Intermediate Non-brooding 0.000304
73 Low Non-brooding 0.000291
74 Low Brooding_wo_embryos 0.000507
75 Low Non-brooding 0.000462
76 Intermediate Non-brooding 0.000127
77 Intermediate Brooding_w_embryos 0.000804
78 Intermediate Brooding_w_embryos 0.000446
79 Intermediate Brooding_w_embryos 0.000747
80 Intermediate Brooding_wo_embryos 0.000297
81 Intermediate Brooding_wo_embryos 0.000308
82 Intermediate Brooding_wo_embryos 0.000348
83 Low Non-brooding 0.000500
84 Low Brooding_wo_embryos 0.000512
85 Intermediate Brooding_w_embryos 0.000822
86 Intermediate Brooding_w_embryos 0.00108
87 Intermediate Brooding_wo_embryos 0.000436
88 Intermediate Brooding_wo_embryos 0.000560
89 Intermediate Brooding_w_embryos 0.000871
90 Intermediate Brooding_wo_embryos 0.000265
91 Low Brooding_w_embryos 0.000485
92 Low Brooding_wo_embryos 0.000241
93 Low Non-brooding 0.000608
94 Low Non-brooding 0.000233
95 Low Non-brooding 0.000481
96 Low Brooding_w_embryos 0.00106
97 Low Brooding_wo_embryos 0.000596
98 Intermediate Non-brooding 0.000254
99 Low Non-brooding 0.000596
100 Low Non-brooding 0.000481
101 Low Brooding_w_embryos 0.000588
102 Low Brooding_w_embryos 0.000574
103 Low Brooding_w_embryos 0.00132
104 Low Brooding_wo_embryos 0.0000973
105 Low Brooding_wo_embryos 0.000281
106 Low Brooding_wo_embryos 0.000291
107 Low Non-brooding 0.000265
108 Low Non-brooding 0.000158
109 Intermediate Brooding_w_embryos 0.00107
110 Intermediate Brooding_w_embryos 0.000415
111 Intermediate Brooding_w_embryos 0.000686
112 Intermediate Brooding_w_embryos 0.000583
113 Intermediate Brooding_w_embryos 0.000852
114 Intermediate Brooding_wo_embryos 0.000565
115 Intermediate Brooding_wo_embryos 0.000137
116 Intermediate Brooding_wo_embryos 0.000314
117 Intermediate Brooding_wo_embryos 0.000295
118 Intermediate Brooding_wo_embryos 0.000355
119 Intermediate Non-brooding 0.000347
120 Intermediate Non-brooding 0.000676
121 Intermediate Non-brooding 0.000347
122 Low Brooding_w_embryos 0.000682
123 Low Brooding_wo_embryos 0.000298
124 Low Non-brooding 0.000639
125 Low Non-brooding 0.000368
126 Intermediate Brooding_w_embryos 0.000974
127 Intermediate Brooding_wo_embryos 0.000460
128 Intermediate Non-brooding 0.000340
129 Intermediate Brooding_w_embryos 0.0006
130 Intermediate Brooding_w_embryos 0.000706
131 Intermediate Brooding_wo_embryos 0.000351
132 Intermediate Brooding_wo_embryos 0.000300
133 Intermediate Non-brooding 0.000382
134 Low Brooding_wo_embryos 0.000422
135 Low Non-brooding 0.000405
136 Low Non-brooding 0.000300
137 Low Brooding_w_embryos 0.000839
138 Low Brooding_wo_embryos 0.000580
139 Intermediate Brooding_w_embryos 0.0007
140 Intermediate Brooding_wo_embryos 0.000241
141 Intermediate Non-brooding 0.000413
142 Intermediate Non-brooding 0.0000462
143 Low Brooding_w_embryos 0.00106
144 Low Brooding_wo_embryos 0.000408
145 Low Non-brooding 0.000239
146 Low Non-brooding 0.000416
147 Low Non-brooding 0.000330
148 Low Non-brooding 0.000365
149 Intermediate Non-brooding 0.000317
150 Low Non-brooding 0.000414
151 Low Non-brooding 0.000434
152 Intermediate Non-brooding 0.0000394
153 Intermediate Brooding_w_embryos 0.000722
154 Intermediate Brooding_wo_embryos 0.000299
155 Low Brooding_w_embryos 0.00104
156 Low Brooding_wo_embryos 0.000404
157 Low Non-brooding 0.000238
158 Intermediate Brooding_w_embryos 0.000757
159 Intermediate Brooding_w_embryos 0.000991
160 Intermediate Brooding_wo_embryos 0.000304
161 Intermediate Brooding_wo_embryos 0.000332
162 Intermediate Non-brooding 0.000239
163 Intermediate Non-brooding 0.000494
164 Intermediate Non-brooding 0.000269
165 Low Brooding_w_embryos 0.000839
166 Low Brooding_wo_embryos 0.000392
167 Low Non-brooding 0.000433
168 Low Non-brooding 0.000506
169 Intermediate Non-brooding 0.000449
170 Intermediate Non-brooding 0.000180
171 Low Non-brooding 0.000406
172 Intermediate Brooding_w_embryos 0.000944
173 Intermediate Brooding_w_embryos 0.000602
174 Intermediate Brooding_wo_embryos 0.000452
175 Intermediate Brooding_wo_embryos 0.000331
176 Intermediate Non-brooding 0.000260
177 Low Non-brooding 0.000299
178 Intermediate Brooding_w_embryos 0.000797
179 Intermediate Brooding_w_embryos 0.000619
180 Intermediate Brooding_wo_embryos 0.000391
181 Intermediate Brooding_wo_embryos 0.000358
182 Low Non-brooding 0.000640
183 Intermediate Brooding_w_embryos 0.000799
184 Intermediate Brooding_wo_embryos 0.000340
185 Low Brooding_w_embryos 0.000779
186 Low Brooding_w_embryos 0.000769
187 Low Brooding_wo_embryos 0.000304
188 Low Brooding_wo_embryos 0.000450
189 Intermediate Brooding_w_embryos 0.000609
190 Intermediate Brooding_wo_embryos 0.000376
191 Intermediate Non-brooding 0.000313
192 Low Brooding_wo_embryos 0.000456
193 Intermediate Brooding_w_embryos 0.000751
194 Intermediate Brooding_w_embryos 0.000453
195 Intermediate Brooding_wo_embryos 0.000378
196 Intermediate Brooding_wo_embryos 0.000200
197 Intermediate Brooding_w_embryos 0.000563
198 Intermediate Brooding_wo_embryos 0.000342
199 Low Non-brooding 0.000485
200 Intermediate Brooding_w_embryos 0.00109
201 Intermediate Brooding_wo_embryos 0.000567
202 Low Brooding_w_embryos 0.00096
203 Low Brooding_wo_embryos 0.000598
204 Intermediate Brooding_w_embryos 0.00063
205 Intermediate Brooding_wo_embryos 0.000408
206 Low Brooding_w_embryos 0.00133
207 Low Brooding_wo_embryos 0.000517
208 Intermediate Brooding_w_embryos 0.00108
209 Intermediate Brooding_wo_embryos 0.000557", header = TRUE)
df$rn <- NULL
stat.test2 <- tibble::tribble(
~group1, ~group2, ~p.adj,
"Intermediate Non-brooding", "Low Non-brooding", 0.6991,
"Intermediate Non-brooding", "Intermediate Brooding_wo_embryos", 1.0000,
"Intermediate Non-brooding", "Low Brooding_wo_embryos", 1.0000,
"Intermediate Non-brooding", "Intermediate Brooding_w_embryos", 0.0001,
"Intermediate Non-brooding", "Low Brooding_w_embryos", 0.0001,
"Low Non-brooding", "Intermediate Brooding_wo_embryos", 1.0000,
"Low Non-brooding", "Low Brooding_wo_embryos", 1.0000,
"Low Non-brooding", "Intermediate Brooding_w_embryos", 0.0001,
"Low Non-brooding", "Low Brooding_w_embryos", 0.0001,
"Intermediate Brooding_wo_embryos", "Low Brooding_wo_embryos", 1.0000,
"Intermediate Brooding_wo_embryos", "Intermediate Brooding_w_embryos", 0.0001,
"Intermediate Brooding_wo_embryos", "Low Brooding_w_embryos", 0.0001,
"Low Brooding_wo_embryos", "Intermediate Brooding_w_embryos", 0.0001,
"Low Brooding_wo_embryos", "Low Brooding_w_embryos", 0.0001,
"Intermediate Brooding_w_embryos", "Low Brooding_w_embryos", 1.0000)
Figure:
ggplot(df, aes(x=interaction(P_treatment, Reproductive, sep = " "),
y=Total_Phosphorus)) +
geom_violin(aes(fill = P_treatment),
width = 1) +
geom_boxplot(position = position_dodge(width = 1), width = 0.1, color="black", alpha=0.5) +
stat_pvalue_manual(stat.test2, y.position = 0.00125, step.increase = 0.1, label = "p.adj") +
theme(axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1))
Created on 2025-03-20 with reprex v2.1.1
Does that work for your use-case?
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