None of my ggtern plots appear in the PDF when I am kniting the R Markdown script I have written. The R/ggtern script works well. I have read many posts on the Internet but none of these could help me to fix this issue. The plots still not appear in the final pdf. Hown can I fix this?
---
title: xxx
subtitle: xxx
author: "xxx"
date: "27/07/2019"
output: pdf_document
---
```{r setup, include=FALSE} #open chunk
knitr::opts_chunk$set(echo = TRUE, error = TRUE, eval = FALSE)
``` #close chunk
``` #open chunk
{r base3, echo=FALSE}
plot(base3)
``` #close chunk
#ggtern 3 zones
points3 <- data.frame(
rbind(
c(1,1.000,0.000,0.000),
c(2,0.500,0.500,0.000),
c(3,0.500,0.000,0.500),
c(4,0.500,0.500,0.500),
c(5,0.000,1.000,0.000),
c(6,0.000,0.500,0.500),
c(7,0.000,0.000,1.000)
)
)
colnames(points3)=c("IDPoint","T","L","R")
#Give each Polygon a number
polygon.labels3 <- data.frame(Label3=c("O","P","N"))
polygon.labels3$IDLabel=1:nrow(polygon.labels3)
#Create a map of polygons to points
polygons3 <- data.frame(
rbind(
c(1,1),c(1,2),c(1,4),c(1,3),
c(2,2),c(2,4),c(2,6),c(2,5),
c(3,3),c(3,7),c(3,6),c(3,4)
)
)
polygons3$PointOrder <- 1:nrow(polygons3)
colnames(polygons3)=c("IDLabel","IDPoint","PointOrder")
#Merge the three sets together to create a master set.
df3 <- merge(polygons3,points3)
df3 <- merge(df3,polygon.labels3)
df3 <- df3[order(df3$PointOrder),]
#Determine the Labels Data
Labs3=ddply(df3,"Label3",function(x){c(c(mean(x$T),mean(x$L),mean(x$R)))})
colnames(Labs3)=c("Label","T","L","R")
#Build the final plot
base3 <- ggtern(data=df3,aes(L,T,R)) +
geom_polygon(aes(group=Label3),color="black",alpha=0) +
geom_text(data=Labs3,aes(label=Label),size=3,color="black") +
theme_bw() +
tern_limits(labels=c(10,20,30,40,50,60,70,80,90,100),breaks=seq(0.1,1,by=0.1)) +
theme_clockwise() +
theme_showarrows() +
labs(title = "Test",Tarrow = "% Oui",Larrow = "% Peut-être",Rarrow = "% Non") +
theme(tern.axis.arrow=element_line(size=1,color="black")) +
labs(title="Diagramme ternaire 3 zones",T="Oui",L="Peut-être",R="Non")
I expect the plots to be displayed in the final pdf.
Here is a screenshot of my .rmd document:
At first I couldn't run your code since you put comments after the chunk options (e.g. deleted #open chunk). Then I reordered your code. The plot should be ploted after creating it. And the code to create the plot should be inside the r chunk too. You also need to add message=FALSEto the chunk options to avoid having the message from the functions printed. I also had to load the two packages plyrand ggtern.
The following code worked for me.
```
---
title: xxx
subtitle: xxx
author: "xxx"
date: "27/07/2019"
output: pdf_document
---
```{r base3, echo=FALSE, message=FALSE}
library(plyr)
library(ggtern)
#ggtern 3 zones
points3 <- data.frame(
rbind(
c(1,1.000,0.000,0.000),
c(2,0.500,0.500,0.000),
c(3,0.500,0.000,0.500),
c(4,0.500,0.500,0.500),
c(5,0.000,1.000,0.000),
c(6,0.000,0.500,0.500),
c(7,0.000,0.000,1.000)
)
)
colnames(points3)=c("IDPoint","T","L","R")
#Give each Polygon a number
polygon.labels3 <- data.frame(Label3=c("O","P","N"))
polygon.labels3$IDLabel=1:nrow(polygon.labels3)
#Create a map of polygons to points
polygons3 <- data.frame(
rbind(
c(1,1),c(1,2),c(1,4),c(1,3),
c(2,2),c(2,4),c(2,6),c(2,5),
c(3,3),c(3,7),c(3,6),c(3,4)
)
)
polygons3$PointOrder <- 1:nrow(polygons3)
colnames(polygons3)=c("IDLabel","IDPoint","PointOrder")
#Merge the three sets together to create a master set.
df3 <- merge(polygons3,points3)
df3 <- merge(df3,polygon.labels3)
df3 <- df3[order(df3$PointOrder),]
#Determine the Labels Data
Labs3=ddply(df3,"Label3",function(x){c(c(mean(x$T),mean(x$L),mean(x$R)))})
colnames(Labs3)=c("Label","T","L","R")
#Build the final plot
base3 <- ggtern(data=df3,aes(L,T,R)) +
geom_polygon(aes(group=Label3),color="black",alpha=0) +
geom_text(data=Labs3,aes(label=Label),size=3,color="black") +
theme_bw() +
tern_limits(labels=c(10,20,30,40,50,60,70,80,90,100),breaks=seq(0.1,1,by=0.1)) +
theme_clockwise() +
theme_showarrows() +
labs(title = "Test",Tarrow = "% Oui",Larrow = "% Peut-être",Rarrow = "% Non") +
theme(tern.axis.arrow=element_line(size=1,color="black")) +
labs(title="Diagramme ternaire 3 zones",T="Oui",L="Peut-être",R="Non")
plot(base3)
```