7/2/2019 r - Tukeys post-hoc on ggplot boxplot - Stack Overflow

Tukeys post-hoc on ggplot boxplot

Ok, so I think I'm pretty close with this, but I'm getting an error when I try to construct my box plot
at the end. My goal is to place letters denoting statistical relationships among the time points
2 above each boxplot. I've seen two discussion of this on this site, and can reproduce the results
from their code, but can't apply it to my dataset.

Packages

2 library(ggplot2)
library(multcompView)
library(plyr)

Here is my data:

dput(WaterConDryMass)
structure(list(ChillTime = structure(c(1L, 1L, 1L, 1L, 2L, 2L,
2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L), .Label = c("Pre_chill",
"6", "13", "24", "Post_chill"), class = "factor"), dmass = c(0.22,
0.19, 0.34, 0.12, 0.23, 0.33, 0.38, 0.15, 0.31, 0.34, 0.45, 0.48,
0.59, 0.54, 0.73, 0.69, 0.53, 0.57, 0.39, 0.8)), .Names = c("ChillTime",
"dmass"), row.names = c(NA, -20L), class = "data.frame")

ANOVA and Tukey Post-hoc

Model4 <- aov(dmass~ChillTime, data=WaterConDryMass)

tHSD <- TukeyHSD(Model4, ordered = FALSE, conf.level = 0.95)
plot(tHSD , las=1 , col="brown" )

Function:

generate_label_df <- function(TUKEY, flev){

# Extract labels and factor levels from Tukey post-hoc

Tukey.levels <- TUKEY[[flev]][,4]
Tukey.labels <- multcompLetters(Tukey.levels)['Letters']
plot.labels <- names(Tukey.labels[['Letters']])

boxplot.df <- ddply(WaterConDryMass, flev, function (x) max(fivenum(x$y)) + 0.2)

# Create a data frame out of the factor levels and Tukey's homogenous group letters
plot.levels <- data.frame(plot.labels, labels = Tukey.labels[['Letters']],
stringsAsFactors = FALSE)

# Merge it with the labels

labels.df <- merge(plot.levels, boxplot.df, by.x = 'plot.labels', by.y = flev, sort =
FALSE)
return(labels.df)
}

Boxplot:

ggplot(WaterConDryMass, aes(x = ChillTime, y = dmass)) +

geom_blank() +
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theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) +
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labs(x = 'Time (weeks)', y = 'Water Content (DM %)') +

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7/2/2019 r - Tukeys post-hoc on ggplot boxplot - Stack Overflow
ggtitle(expression(atop(bold("Water Content"), atop(italic("(Dry Mass)"), "")))) +
theme(plot.title = element_text(hjust = 0.5, face='bold')) +
annotate(geom = "rect", xmin = 1.5, xmax = 4.5, ymin = -Inf, ymax = Inf, alpha = 0.6,
fill = "grey90") +
geom_boxplot(fill = 'green2', stat = "boxplot") +
geom_text(data = generate_label_df(tHSD), aes(x = plot.labels, y = V1, label =
labels)) +
geom_vline(aes(xintercept=4.5), linetype="dashed") +
theme(plot.title = element_text(vjust=-0.6))

Error:

Error in HSD[[flev]] : invalid subscript type 'symbol'

r ggplot2 boxplot

asked Jun 23 '17 at 2:33

Alex
44 2 8

1 Answer

¿No encuentras la respuesta? Pregunta en Stack Overflow en español. ✕

I think I found the tutorial you are following, or something very similar. You would probably be
best to copy and paste this whole thing into your work space, function and all, to avoid missing a
2 few small differences.

Basically I have followed the tutorial (http://www.r-graph-gallery.com/84-tukey-test/) to the letter

and added a few necessary tweaks at the end. It adds a few extra lines of code, but it works.

generate_label_df <- function(TUKEY, variable){

# Extract labels and factor levels from Tukey post-hoc

Tukey.levels <- TUKEY[[variable]][,4]
Tukey.labels <- data.frame(multcompLetters(Tukey.levels)['Letters'])

#I need to put the labels in the same order as in the boxplot :

Tukey.labels$treatment=rownames(Tukey.labels)
Tukey.labels=Tukey.labels[order(Tukey.labels$treatment) , ]
return(Tukey.labels)
}

model=lm(WaterConDryMass$dmass~WaterConDryMass$ChillTime )
ANOVA=aov(model)

# Tukey test to study each pair of treatment :

TUKEY <- TukeyHSD(x=ANOVA, 'WaterConDryMass$ChillTime', conf.level=0.95)

labels<-generate_label_df(TUKEY , "WaterConDryMass$ChillTime")#generate labels using

function

names(labels)<-c('Letters','ChillTime')#rename columns for merging

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our Termsyvalue<-aggregate(.~ChillTime,
of Service. data=WaterConDryMass, mean)# obtain letter position for y
axis using means

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7/2/2019 r - Tukeys post-hoc on ggplot boxplot - Stack Overflow

final<-merge(labels,yvalue) #merge dataframes

ggplot(WaterConDryMass, aes(x = ChillTime, y = dmass)) +

geom_blank() +
theme_bw() +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) +
labs(x = 'Time (weeks)', y = 'Water Content (DM %)') +
ggtitle(expression(atop(bold("Water Content"), atop(italic("(Dry Mass)"), "")))) +
theme(plot.title = element_text(hjust = 0.5, face='bold')) +
annotate(geom = "rect", xmin = 1.5, xmax = 4.5, ymin = -Inf, ymax = Inf, alpha = 0.6,
fill = "grey90") +
geom_boxplot(fill = 'green2', stat = "boxplot") +
geom_text(data = final, aes(x = ChillTime, y = dmass, label =
Letters),vjust=-3.5,hjust=-.5) +
geom_vline(aes(xintercept=4.5), linetype="dashed") +
theme(plot.title = element_text(vjust=-0.6))

answered Jun 23 '17 at 4:20

J.Con
1,936 1 14 34

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