Hello everyone, I hope you all are very well. Some time ago I asked for help to create a multiple boxplot in a graph, this variables were analized with the package ggsignif.
As the following example:
Now I am using another statistical analysis (tukeyHSD, with letters) but I could not put all the images of my variables together.
Is it possible to do it with this statistical analysis?
An apology for pasting my code in parts, I did it this way because it gave me this error: Error: pandoc document conversion failed with error 1
library(vegan)
#> Loading required package: permute
#> Loading required package: lattice
#> This is vegan 2.5-5
library(readxl)
library(multcompView)
library(ggplot2)
library(plyr)
bpdata <- data.frame(
DO = c(4.24, 2.58, 2.85, 3.81, 2.64, 4.61, 5.74, 3.69, 4.24,
2.66, 2.85, 3.81, 2.64, 4.61, 5.74, 3.69, 2.51, 2.66,
3.14, 2.92, 1.83, 1.82, 3.02, 3.3, 2.51, 3.04, 2.85,
2.92, 1.83, 1.82, 3.02, 3.3, 4.24, 3.04, 2.85, 3.81, 2.64,
4.61, 5.74, 3.69, 4.24, 2.09, 2.98, 3.81, 1.83, 1.82,
3.02, 3.3, 2.51, 2.09, 2.98, 8.17, 2.63, 7.69, 3.07, 3.7,
2.51, 3.04, 2.18, 8.17, 2.63, 7.69, 3.07, 3.7, 2.58,
2.09, 2.18, 2.16, 1.7, 6.8, 1.95, 4.28, 2.58, 2.09, 2.98,
2.16, 1.7, 6.8, 1.95, 4.28, 2.66, 3.14, 2.18, 8.17, 2.63,
7.69, 3.07, 3.7, 2.66, 3.14, 2.92, 2.16, 1.7, 6.8,
1.95, 4.28),
pH = c(9.94, 10.06, 9.98, 9.07, 8.99, 8.93, 9.24, 9.32, 9.94,
10, 9.98, 9.07, 8.99, 8.93, 9.24, 9.32, 10.04, 10, 10,
9.06, 8.99, 8.92, 9.18, 9.32, 10.04, 9.96, 9.98, 9.06,
8.99, 8.92, 9.18, 9.32, 9.94, 9.96, 9.98, 9.07, 8.99,
8.93, 9.24, 9.32, 9.94, 9.95, 10.09, 9.07, 8.99, 8.92,
9.18, 9.32, 10.04, 9.95, 10.09, 9.04, 9, 9.53, 9.31, 9.14,
10.04, 9.96, 9.97, 9.04, 9, 9.53, 9.31, 9.14, 10.06,
9.95, 9.97, 8.96, 9.02, 9.51, 9.39, 8.85, 10.06, 9.95,
10.09, 8.96, 9.02, 9.51, 9.39, 8.85, 10, 10, 9.97, 9.04, 9,
9.53, 9.31, 9.14, 10, 10, 9.06, 8.96, 9.02, 9.51, 9.39,
8.85),
Temperature = c(24.48, 24.95, 24.01, 26.67, 24.01, 23.5, 24.46, 24.65,
24.48, 24.92, 24.01, 26.67, 24.01, 23.5, 24.46, 24.65,
24.35, 24.92, 24, 26.46, 23.99, 23.43, 24.14, 24.67,
24.35, 24.04, 24.01, 26.46, 23.99, 23.43, 24.14, 24.67,
24.48, 24.04, 24.01, 26.67, 24.01, 23.5, 24.46, 24.65,
24.48, 24.01, 24.36, 26.67, 23.99, 23.43, 24.14, 24.67,
24.35, 24.01, 24.36, 24.88, 24.7, 26.14, 24.19, 22.65,
24.35, 24.04, 24.4, 24.88, 24.7, 26.14, 24.19, 22.65, 24.95,
24.01, 24.4, 24.3, 24.72, 26.15, 23.9, 20.65, 24.95,
24.01, 24.36, 24.3, 24.72, 26.15, 23.9, 20.65, 24.92, 24,
24.4, 24.88, 24.7, 26.14, 24.19, 22.65, 24.92, 24,
26.46, 24.3, 24.72, 26.15, 23.9, 20.65),
Turbidity = c(87.3, 95.2, 98.8, 24.9, 43.1, 49.1, 68.6, 69.8, 87.3,
113, 98.8, 24.9, 43.1, 49.1, 68.6, 69.8, 87.7, 113,
96.9, 39.7, 49, 47.6, 66.6, 74.1, 87.7, 98.5, 98.8, 39.7,
49, 47.6, 66.6, 74.1, 87.3, 98.5, 98.8, 24.9, 43.1,
49.1, 68.6, 69.8, 87.3, 95.9, 97.2, 24.9, 49, 47.6, 66.6,
74.1, 87.7, 95.9, 97.2, 46.9, 37.2, 74.2, 69.9, 71.3,
87.7, 98.5, 100.6, 46.9, 37.2, 74.2, 69.9, 71.3, 95.2, 95.9,
100.6, 42, 36.1, 74.4, 44.4, 71.3, 95.2, 95.9, 97.2,
42, 36.1, 74.4, 44.4, 71.3, 113, 96.9, 100.6, 46.9, 37.2,
74.2, 69.9, 71.3, 113, 96.9, 39.7, 42, 36.1, 74.4, 44.4,
71.3),
ORP = c(97, 108.4, 102.9, 94, 63.9, 64.7, 40.3, 48.1, 97,
111.9, 102.9, 94, 63.9, 64.7, 40.3, 48.1, 91.3, 111.9,
108, 23.7, 64.1, 60.4, 40.6, 49.8, 91.3, 98.9, 102.9,
23.7, 64.1, 60.4, 40.6, 49.8, 97, 98.9, 102.9, 94, 63.9,
64.7, 40.3, 48.1, 97, 92.8, 106.9, 94, 64.1, 60.4, 40.6,
49.8, 91.3, 92.8, 106.9, 90.4, 74.9, 67.7, 42, 37.1,
91.3, 98.9, 102.7, 90.4, 74.9, 67.7, 42, 37.1, 108.4,
92.8, 102.7, 53, 63.4, 73.9, 42, 37.5, 108.4, 92.8, 106.9,
53, 63.4, 73.9, 42, 37.5, 111.9, 108, 102.7, 90.4, 74.9,
67.7, 42, 37.1, 111.9, 111.9, 23.7, 53, 63.4, 73.9, 42,
37.5),
Ammonium = c(4.46, 4.62, 4.37, 5.6, 3.38, 3.21, 1.93, 2.21, 4.46,
4.75, 4.37, 5.6, 3.38, 3.21, 1.93, 2.21, 4.5, 4.75,
4.48, 7.64, 3.18, 3.09, 2.19, 2.14, 4.5, 3.97, 4.37, 7.64,
3.18, 3.09, 2.19, 2.14, 4.46, 3.97, 4.37, 5.6, 3.38,
3.21, 1.93, 2.21, 4.46, 4.06, 4.43, 5.6, 3.18, 3.09, 2.19,
2.14, 4.5, 4.06, 4.43, 2.81, 4.2, 4.5, 1.99, 2.07, 4.5,
3.97, 5.47, 2.81, 4.2, 4.5, 1.99, 2.07, 4.62, 4.06,
5.47, 3.19, 3.97, 3.3, 3.38, 1.18, 4.62, 4.06, 4.43, 3.19,
3.97, 3.3, 3.38, 1.18, 4.75, 4.48, 5.47, 2.81, 4.2, 4.5,
1.99, 2.07, 4.75, 4.48, 7.64, 3.19, 3.97, 3.3, 3.38,
1.18),
Nitrates = c(3.6, 3.98, 3.57, 3.53, 2.55, 2.28, 0.71, 1.2, 3.6,
3.21, 3.57, 3.53, 2.55, 2.28, 0.71, 1.2, 3.36, 3.21,
3.76, 3.66, 2.44, 2.06, 0.67, 0.87, 3.36, 4.35, 3.57,
3.66, 2.44, 2.06, 0.67, 0.87, 3.6, 4.35, 3.57, 3.53, 2.55,
2.28, 0.71, 1.2, 3.6, 3.68, 3.34, 3.53, 2.44, 2.06,
0.67, 0.87, 3.36, 3.68, 3.34, 2.25, 2.99, 1.3, 0.74, 0.68,
3.36, 4.35, 4.11, 2.25, 2.99, 1.3, 0.74, 0.68, 3.98,
3.68, 4.11, 2.1, 2.55, 1.11, 0.69, 0.69, 3.98, 3.68, 3.34,
2.1, 2.55, 1.11, 0.69, 0.69, 3.21, 3.76, 4.11, 2.25,
2.99, 1.3, 0.74, 0.68, 3.21, 3.76, 3.66, 2.1, 2.55, 1.11,
0.69, 0.69),
BGA = c(279133, 279113, 265304, 11603, 218471, 226658, 267389,
267144, 279133, 270193, 265304, 11603, 218471, 226658,
267389, 267144, 267716, 270193, 279119, 66608, 213497,
242331, 267007, 261363, 267716, 279109, 265304, 66608,
213497, 242331, 267007, 261363, 279133, 279109, 265304,
11603, 218471, 226658, 267389, 267144, 279133, 279100,
279099, 11603, 213497, 242331, 267007, 261363, 267716,
279100, 279099, 246979, 169175, 272332, 269519, 272096,
267716, 279109, 278137, 246979, 169175, 272332, 269519,
272096, 279113, 279100, 278137, 174271, 159046, 271503,
261124, 271303, 279113, 279100, 279099, 174271, 159046,
271503, 261124, 271303, 270193, 279119, 278137, 246979,
169175, 272332, 269519, 272096, 270193, 279119, 66608,
174271, 159046, 271503, 261124, 271303),
Chlrophyll = c(36.6, 38.9, 40, 44, 35, 32.8, 44, 44.8, 36.6, 39.8,
40, 44, 35, 32.8, 44, 44.8, 39.6, 39.8, 38.5, 45.1,
42.2, 50.2, 43.6, 45.1, 39.6, 43, 40, 45.1, 42.2, 50.2,
43.6, 45.1, 36.6, 43, 40, 44, 35, 32.8, 44, 44.8, 36.6,
50, 43, 44, 42.2, 50.2, 43.6, 45.1, 39.6, 50, 43, 34,
38.4, 58.5, 44.3, 40, 39.6, 43, 53.8, 34, 38.4, 58.5, 44.3,
40, 38.9, 50, 53.8, 50.3, 55.9, 51.3, 68.2, 34.2, 38.9,
50, 43, 50.3, 55.9, 51.3, 68.2, 34.2, 39.8, 38.5, 53.8,
34, 38.4, 58.5, 44.3, 40, 39.8, 38.5, 45.1, 50.3, 55.9,
51.3, 68.2, 34.2),
Month = as.factor(c("July", "July", "July", "August", "August", "August",
"September", "September", "July", "July", "July",
"August", "August", "August", "September", "September",
"July", "July", "July", "August", "August", "August",
"September", "September", "July", "July", "July", "August",
"August", "August", "September", "September", "July",
"July", "July", "August", "August", "August", "September",
"September", "July", "July", "July", "August", "August",
"August", "September", "September", "July", "July",
"July", "August", "August", "September", "September",
"September", "July", "July", "July", "August", "August",
"September", "September", "September", "July", "July",
"July", "August", "August", "September", "September",
"September", "July", "July", "July", "August", "August",
"September", "September", "September", "July", "July", "July",
"August", "August", "September", "September",
"September", "July", "July", "August", "August", "August",
"September", "September", "September"))
)
Created on 2019-11-13 by the reprex package (v0.3.0)
bpdata$Month <- factor(bpdata$Month,
levels = c("July", "August", "September"))
#> Error in factor(bpdata$Month, levels = c("July", "August", "September")): objeto 'bpdata' no encontrado
res.aov <- aov(pH~Month, data = bpdata)
#> Error in terms.formula(formula, "Error", data = data): objeto 'bpdata' no encontrado
summary(res.aov)
#> Error in summary(res.aov): objeto 'res.aov' no encontrado
TukeyHSD(res.aov)
#> Error in TukeyHSD(res.aov): objeto 'res.aov' no encontrado
tHSD <- TukeyHSD(res.aov, ordered = FALSE, conf.level = 0.95)
#> Error in TukeyHSD(res.aov, ordered = FALSE, conf.level = 0.95): objeto 'res.aov' no encontrado
generate_label_df <- function(HSD, flev){
#Extract labels and factor levels from Tukey post-hoc
Tukey.levels <- HSD[[flev]][,4]
Tukey.labels <- multcompLetters(Tukey.levels)['Letters']
plot.labels <- names(Tukey.labels[['Letters']])
# Get highest quantile for Tukey's 5 number summary and add a bit of space to buffer between
# upper quantile and label placement
boxplot.df <- ddply(bpdata, flev, function (x) max(fivenum(x$pH)) + 0.2)
# Create a data frame out of the factor levels and Tukey's homogenous group letters
plot.levels <- data.frame(Month= plot.labels,
labels = Tukey.labels[['Letters']],
stringsAsFactors = FALSE)
# Merge it with the labels
labels.df <- merge(plot.levels, boxplot.df, by.x = 'Month', by.y = flev, sort = FALSE)
return(labels.df)
}
ggplot(bpdata, aes(x=Month, y=pH, fill = Month)) +
geom_boxplot ()+
geom_text(data=generate_label_df(tHSD,'Month'), aes(x = Month, y = V1, label = labels))+
scale_y_continuous(expand = c(0.02,0.02))+
theme_bw()+
theme(panel.grid.major = element_line(colour = "white"),
panel.grid.minor = element_blank(),
panel.background = element_blank(),
plot.title = element_text(hjust = 0.5, size = 14, family = "Tahoma", face = "bold"),
text=element_text(family = "Tahoma", face ="bold"),
axis.title = element_text(face="bold"),
axis.text.x = element_text(colour="black", size = 11),
axis.text.y = element_text(colour="black", size = 9),
axis.line = element_line(size=0.5, colour = "black"))
#> Error in ggplot(bpdata, aes(x = Month, y = pH, fill = Month)): no se pudo encontrar la función "ggplot"
dev.off()
#> null device
#> 1
Created on 2019-11-13 by the reprex package (v0.3.0)
