[R] boxplot notch

[CALUM POLWART]

Unless I'm missing the point, you are sending the summary data MS1s to the
plot.  Is that not a VERY unusual way to do it. Let box plot do the
summary? Otherwise what do you want the notches to show?

On Fri, 16 Aug 2024, 17:21 Chris Evans via R-help, <r-help using r-project.org>
wrote:

> That's not really a reprex Sibylle.  I did try to use it to see if I
> could work out what you were trying to do and help but there is so much
> in there that I suspect is distraction from the notch issue and its
> error message.
>
> Please can you give us something stripped of all unecessary things and
> tell us what you want?
>
> Something like data that we can read as a tribble() or from a dput() of
> your data and then only the packages you actually need for the plot (I
> think tidyverse alone might do) and then a ggplot() call stripped right
> down to what you need and a clear explanation of what you are trying to
> do in the geom_boxplot() call and how it uses the summarised data tibble.
>
> It may even be that if you do that, you will find what's causing the
> problem!  (I speak from bitter experience!!)
>
> Very best (all),
>
> Chris
>
> On 16/08/2024 17:51, SIBYLLE STÖCKLI via R-help wrote:
> > Farm_ID       Jahr    Bio     QI_A
> > 1     2015    1       9.5
> > 2     2018    1       15.7
> > 3     2020    1       21.5
> > 1     2015    1       50.5
> > 2     2018    1       12.9
> > 3     2020    1       11.2
> > 1     2015    1       30.6
> > 2     2018    1       28.7
> > 3     2020    1       29.8
> > 1     2015    1       30.1
> > 2     2018    1       NA
> > 3     2020    1       16.9
> > 1     2015    0       6.5
> > 2     2018    0       7.9
> > 3     2020    0       10.2
> > 1     2015    0       11.2
> > 2     2018    0       18.5
> > 3     2020    0       29.5
> > 1     2015    0       25.1
> > 2     2018    0       16.1
> > 3     2020    0       15.9
> > 1     2015    0       10.1
> > 2     2018    0       8.4
> > 3     2020    0       3.5
> > 1     2015    0       NA
> > 2     2018    0       NA
> > 3     2020    0       3.5
> >
> >
> > Code
> > setwd("C:/Users/Sibylle Stöckli/Desktop/")
> > #.libPaths()
> > getwd()
> >
> > #libraries laden
> > library("ggplot2")
> > library("gridExtra")
> > library(scales)
> > library(nlme)
> > library(arm)
> > library(blmeco)
> > library(stats)
> > library(dplyr)
> > library(ggpubr)
> > library(patchwork)
> > library(plotrix)
> > library(tidyverse)
> > library(dplyr)
> >
> > #read data
> > MS = read.delim("Test1.txt", na.strings="NA")
> > names(MS)
> >
> > MS$Jahr<-as.numeric(MS$Jahr)
> > MS$Bio<-as.factor(MS$Bio)
> > str(MS)
> >
> > ##### boxplot BFF QI
> >
> > MS1<- MS %>% filter(QI_A!="NA") %>% droplevels()
> > MS1$Jahr<-as.factor(MS1$Jahr)
> >
> > MS1s <- MS1 %>%
> >    group_by(MS1$Jahr, MS1$Bio) %>%
> >    summarise(
> >      y0 = quantile(QI_A, 0.05),
> >      y25 = quantile(QI_A, 0.25),
> >      y50 = mean(QI_A),
> >      y75 = quantile(QI_A, 0.75),
> >      y100 = quantile(QI_A, 0.95))
> >
> > MS1s
> > colnames(MS1s)[1]<-"Jahr"
> > colnames(MS1s)[2]<-"Bio"
> > MS1s
> >
> > p1<-ggplot(MS1s, aes(Jahr,  fill = as.factor(Bio))) +
> >    geom_boxplot(
> >      aes(ymin = y0, lower = y25, middle = y50, upper = y75, ymax = y100),
> >      stat = "identity", notch=TRUE
> >    ) +
> >    theme(panel.background = element_blank())+
> >    theme(axis.line = element_line(colour = "black"))+
> >    theme(axis.text=element_text(size=18))+
> >    theme(axis.title=element_text(size=20))+
> >    ylab("Anteil BFF an LN [%]") +xlab("Jahr")+
> >    scale_color_manual(values=c("red","darkgreen"), labels=c("ÖLN",
> "BIO"))+
> >    scale_fill_manual(values=c("red","darkgreen"), labels= c("ÖLN",
> "BIO"))+
> >    theme(legend.title = element_blank())+
> >    theme(legend.text=element_text(size=20))
> > p1<-p1 + expand_limits(y=c(0, 80))
> > p1
> --
> Chris Evans (he/him)
> Visiting Professor, UDLA, Quito, Ecuador & Honorary Professor,
> University of Roehampton, London, UK.
> Work web site: https://www.psyctc.org/psyctc/
> CORE site: http://www.coresystemtrust.org.uk/
> Personal site: https://www.psyctc.org/pelerinage2016/
> Emeetings (Thursdays):
> https://www.psyctc.org/psyctc/booking-meetings-with-me/
> (Beware: French time, generally an hour ahead of UK)
> <https://ombook.psyctc.org/book>
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>
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