r - knitr plots: Points (geom_point(), pch=20, pch=19...) not showing -
i'm bit troubled behaviour of knitr. working example should show 4 plots, showing same data using 2 different plot-methods.
preamble:
\documentclass{article} the first 2 plots made using plot command of r-base:
<<one.one,fig.width=4,fig.height=3,fil.align='center',fig.show='asis'>>= par(mar=c(4,4,1,1),mgp=c(2,1,0),cex=0.8) plot(cars,pch=20,col='darkgray') @ <<one.two,fig.width=4,fig.height=3,fil.align='center',fig.show='asis'>>= par(mar=c(4,4,1,1),mgp=c(2,1,0),cex=0.8) plot(cars,pch=18,col='darkgray') @ the outputs given (deleted):
for same plot ggplot2 code examples are:
<<two.one,fig.width=4,fig.height=3,fil.align='center',fig.show='asis'>>= library(ggplot2) test1<-ggplot(cars,aes(x=speed,y=dist)) test2<-test1+geom_smooth(method="lm",se=false,color='red',data=fit) test3<-test2+ ggtitle("") + geom_point(size=1,colour='red') test3 @ <<two.two,fig.width=4,fig.height=3,fil.align='center',fig.show='asis'>>= test1<-ggplot(cars,aes(x=speed,y=dist)) test2<-test1+geom_smooth(method="lm",se=false,color='red',data=fit) test3<-test2+ ggtitle("") + geom_point(size=1,colour='red',shape=3) test3 @ and outputs (deleted):
even using tikzdevice doesn't solve issue me. problem exists me since nov. last year, @ least far can remember. tried solving reading yihui xie's book, used examples website, failed.
so: has seen same problem , has come solution it? hint pointing in direction might help.
my system:
win 7, miktex2.9 (packages updated on 15.01.2016), texstudio 2.10.6, r3.2.2 (packages updated on 15.01.2016).
edit:
as asked cl, updated r , packages right along, too. below find mwe. problem of not-showing data points when using pch=20 ; pch=19, geom_point() persistent long don't choose graphics device explictly. when using tikzdevice , saving plots *.tex, data points show. show when putting dev='tikz' chunk options. other graphic devices seem work well.
the mwe is:
\documentclass{article} \usepackage{graphicx} \usepackage{tikz} \begin{document} \begin{verbatim} chunk options: fig.width=4,fig.height=3,fig.align='center',fig.show='asis' \end{verbatim} <<one.one,fig.width=4,fig.height=3,fig.align='center',fig.show='asis'>>= library(knitr) par(mar=c(4,4,1,1),mgp=c(2,1,0),cex=0.8) plot(cars,pch=20,col='darkgray') fit<-lm(dist~speed, data=cars) abline(fit,lwd=1,col='red') par(mar=c(4,4,1,1),mgp=c(2,1,0),cex=0.8) plot(cars,pch=18,col='darkgray') fit<-lm(dist~speed, data=cars) abline(fit,lwd=1,col='red') library(ggplot2) test1<-ggplot(cars,aes(x=speed,y=dist)) test2<-test1+geom_smooth(method="lm",se=false,color='red',data=fit) test3<-test2+ ggtitle("") + geom_point(size=1,colour='red') test3 test1<-ggplot(cars,aes(x=speed,y=dist)) test2<-test1+geom_smooth(method="lm",se=false,color='red',data=fit) test3<-test2+ ggtitle("") + geom_point(size=1,colour='red',shape=3) test3 @ \begin{verbatim} next chunk options: three.one,fig.width=4,fig.height=3,fig.align='center',fig.show='asis' \end{verbatim} <<three.one,fig.width=4,fig.height=3,fig.align='center',fig.show='asis'>>= require(tikzdevice) tikz("three.one.tex",width=4.2,height=3) plot(cars,pch=20,col='darkgray') fit<-lm(dist~speed, data=cars) abline(fit,lwd=1,col='red') dev.off() tikz("four.one.tex",width=4.2,height=3) test1<-ggplot(cars,aes(x=speed,y=dist)) test2<-test1+geom_smooth(method="lm",se=false,color='red',data=fit) test3<-test2+ ggtitle("") + geom_point(size=1,colour='red') test3 dev.off() @ \input{three.one.tex} \input{four.one.tex} \begin{verbatim} next chunk options: five.one,fig.width=4,fig.height=3,fig.align='center',fig.show='asis, dev='tikz' \end{verbatim} <<five.one,fig.width=4,fig.height=3,fig.align='center',fig.show='asis',dev='tikz'>>= plot(cars,pch=20,col='darkgray') abline(fit,lwd=1,col='red') test1<-ggplot(cars,aes(x=speed,y=dist)) test2<-test1+geom_smooth(method="lm",se=false,color='red',data=fit) test3<-test2+ ggtitle("") + geom_point(size=1,colour='red') test3 @ \begin{verbatim} next chunk options: five.one,fig.width=4,fig.height=3,fig.align='center',fig.show='asis, dev=c('png','pdf') \end{verbatim} <<seven.one,fig.width=4,fig.height=3,fig.align='center',fig.show='asis',dev=c('png', 'pdf')>>= plot(cars,pch=20,col='darkgray') abline(fit,lwd=1,col='red') test1<-ggplot(cars,aes(x=speed,y=dist)) test2<-test1+geom_smooth(method="lm",se=false,color='red',data=fit) test3<-test2+ ggtitle("") + geom_point(size=1,colour='red') test3 @ \end{document} if issue not reproducible, make peace , ignore it. if it's reproducible, i'm curious solution might like.
along tests, came issue , found problem stated @ least 1 other tex-user, too: knitr , latex package xcolor don't seem best of friends.
thank's again.
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