In order to "convert" a ggplot2 graphic to a pdf LaTeX graphic with the tikzDevice package, I'd like to put the axis ticks labels between two $. Of course I can do it if I specify manually the tick labels, but how to do when using the automatic tick labels ? (in particular when using dates on the x-axis it is hard to specify manually the labels).
Update - solution with axis labels formatter
Based on #agstudy's answer, I have written the dollarify() formatter for numerical labels:
dollarify <- function(){
function(x) paste0("$",x,"$")
}
and the datify() formatter for dates:
datify <- function(){
function(x){
split <- stringr::str_split_fixed(as.character(x),"-",3)
out <- character(nrow(split))
for(i in 1:length(out)){
out[i] <- paste0("\\formatdate{", split[i,3], "}{", split[i,2], "}{", split[i,1], "}")
}
out
}
}
which generates a LaTeX code to be used with the datetime package:
\usepackage[ddmmyyyy]{datetime}
Below is a screenshot of a rendering, using the following scale for the x-axis :
scale_x_date(breaks="2 months", labels=datify())
It is not clear what you want to do but I think you are looking for an axis labels formatter.
## forma :you can give here any date format
dollar_date_format <- function (forma = "%H:%M"){
function(x) paste0("$",format(x,forma),"$")
}
Then using some data ( please provide reproducible example next time) you can use it like this:
DF <- data.frame(time=Sys.time()+1:10,count=1:10)
library(ggplot2)
qplot(x=time,y=count,data=DF)+
scale_x_datetime(labels = dollar_date_format(forma = "%M:%S"))+
xlab("Time (dollars)") +
theme(axis.text.x =element_text(size=20))
If you want to generically be able to modify the axis labels, you can run the plot, use ggplot_build() to get the plotted labels back, then add e.g. scale_x_continuous()/scale_x_date() with custom labels on the rendered breaks. You will need to tweak it depending on datatypes (look in the build variable to see what data's available).
You might want to use $x/y.labels or $x/y.major_source depending on datatype
x=c("2013-03-22","2013-04-24","2013-07-01","2013-09-13")
y=c(1,2,3,4)
#any ggplot object
g<-qplot(as.Date(x),y)
#call the rendered axis labels
build<-ggplot_build(g)
xrng<-data.frame(build$panel$ranges[[1]]$x.major_source,stringsAsFactors=FALSE)
yrng<-data.frame(build$panel$ranges[[1]]$y.labels,stringsAsFactors=FALSE)
colnames(xrng)<-"value"
colnames(yrng)<-"value"
#create custom labels
xrng$lab<-paste0("$",row.names(xrng),"$")
yrng$lab<-paste0("$",yrng$value,"$")
#re-render with custom labels
g+scale_x_date(breaks=as.Date(xrng$value),labels=xrng$lab) +
scale_y_continuous(breaks=as.numeric(yrng$value),labels=yrng$lab)
Related
I'm creating a set of functions for enciphering data plots as a hook for data literacy lessons.
For example, this function performs an alphabetic shift of +/- X for any string input
enciphR<-function(x,alg,key=F){
x.vec<-tolower(unlist(strsplit(x,fixed=T,split="")))#all lower case as vector
#define new alphabet
alphabet<-1:26+alg
alphabet.shifted.idx<-sapply(alphabet,function(x) {if(x>26){x-26}else{ if(x<1){x+26}else{x}}})
alphabet.shifted<-letters[alphabet.shifted.idx]
keyMat=cbind(IN=letters,OUT=alphabet.shifted)
#encipher
x1.1<-as.vector(sapply(x.vec,function(s) {
if(!s%in%letters){s}else{#If nonletter, leave it alone, else...
keyMat[match(s,keyMat[,"IN"]),"OUT"]
}},USE.NAMES = F))
x2<-paste0(x1.1,collapse="")
if(key){
out<-list(IN=x,OUT=x2,KEY=keyMat)}
else{
out<-x2
}
return(out)
}
enciphR(letters,+1) yields "bcdefghijklmnopqrstuvwxyza"
I want to feed a ggplot object into another function ggEnciphR(), which uses the enciphR() helper to encode all text elements of that object, according to the supplied cipher algorithm.
So, start with a figure:
data("AirPassengers")
require(ggplot2);require(reshape2)
df <- data.frame(Passengers=as.numeric(AirPassengers), year = as.factor(trunc(time(AirPassengers))), mnth = month.abb[cycle(AirPassengers)])
(gg<-qplot(mnth,Passengers,aes(col=year),data=df)+geom_line(aes(group=year,col=year)))
now I define the ggCiphR function:
ggCiphR<-function(ggGraph,alg){
g<-ggGraph
pass2enciphR=function(x){enciphR(x,alg=alg)}
#process all labels
g$labels<-lapply(g$labels,pass2enciphR)
#process custom legend if present (sometimes works, depending on ggplot object)
try(if(length(g$scales$scales)>0){
for(i in 1:length(g$scales$scales)){
g$scales$scales[[i]]$name=enciphR(g$scales$scales[[i]],alg=alg)
}
})
g
}
ggCiphR(gg,+1)
Yields:
This is getting there. Axis labels and legend title have been enciphered, but not tick values. Also, if my factor was Airline, instead of Year, I'd like that to be sent through enciphR, as well.
I've searched high and wide and cannot for the life of me figure out how to modify x- and y-axis values and factor levels from the gg object. I don't want to have to recast the dataframe and regenerate the ggplot... ideally I can do this programmatically using the gg object. And also, it would (ideally) be flexible enough to work with different classes of data in X & Y. Thoughts?
Does anyone have an idea how is this kind of chart plotted? It seems like heat map. However, instead of using color, size of each cell is used to indicate the magnitude. I want to plot a figure like this but I don't know how to realize it. Can this be done in R or Matlab?
Try scatter:
scatter(x,y,sz,c,'s','filled');
where x and y are the positions of each square, sz is the size (must be a vector of the same length as x and y), and c is a 3xlength(x) matrix with the color value for each entry. The labels for the plot can be input with set(gcf,properties) or xticklabels:
X=30;
Y=10;
[x,y]=meshgrid(1:X,1:Y);
x=reshape(x,[size(x,1)*size(x,2) 1]);
y=reshape(y,[size(y,1)*size(y,2) 1]);
sz=50;
sz=sz*(1+rand(size(x)));
c=[1*ones(length(x),1) repmat(rand(size(x)),[1 2])];
scatter(x,y,sz,c,'s','filled');
xlab={'ACC';'BLCA';etc}
xticks(1:X)
xticklabels(xlab)
set(get(gca,'XLabel'),'Rotation',90);
ylab={'RAPGEB6';etc}
yticks(1:Y)
yticklabels(ylab)
EDIT: yticks & co are only available for >R2016b, if you don't have a newer version you should use set instead:
set(gca,'XTick',1:X,'XTickLabel',xlab,'XTickLabelRotation',90) %rotation only available for >R2014b
set(gca,'YTick',1:Y,'YTickLabel',ylab)
in R, you should use ggplot2 that allows you to map your values (gene expression in your case?) onto the size variable. Here, I did a simulation that resembles your data structure:
my_data <- matrix(rnorm(8*26,mean=0,sd=1), nrow=8, ncol=26,
dimnames = list(paste0("gene",1:8), LETTERS))
Then, you can process the data frame to be ready for ggplot2 data visualization:
library(reshape)
dat_m <- melt(my_data, varnames = c("gene", "cancer"))
Now, use ggplot2::geom_tile() to map the values onto the size variable. You may update additional features of the plot.
library(ggplot2)
ggplot(data=dat_m, aes(cancer, gene)) +
geom_tile(aes(size=value, fill="red"), color="white") +
scale_fill_discrete(guide=FALSE) + ##hide scale
scale_size_continuous(guide=FALSE) ##hide another scale
In R, corrplotpackage can be used. Specifically, you have to use method = 'square' when creating the plot.
Try this as an example:
library(corrplot)
corrplot(cor(mtcars), method = 'square', col = 'red')
Is it possible to change the legend on the plot displayed in Quantmod so that values are displayed rather than the variable name? For example:
library("quantmod")
getSymbols("YHOO")
temp1 <- 6
temp2 <- "SMA"
barChart(YHOO)
addTA(ADX(YHOO, n=temp1, maType=temp2))
The legend that is displayed in the plot is ADX(YHOO, n=temp1, maType=temp2). I would like it to display the specific values instead i.e. ADX(YHOO, n=6, maType='SMA').
There isn't a way to do this automatically with addTA, because it would need to know which of the the parameters of the TA call it needs to evaluate. But you can do it manually by setting the legend= argument yourself.
One way to do it is to use paste (or paste0).
barChart(YHOO)
Legend <- paste0('ADX(YHOO, n=',temp1,', maType=',temp2,')')
addTA(ADX(YHOO, n=temp1, maType=temp2), legend=Legend)
Or you could create and manipulate the call to get what you want.
barChart(YHOO)
callTA <- call("ADX",quote(YHOO),n=temp1,maType=temp2)
eval(call("addTA", callTA, legend=deparse(callTA)))
The following is a partial solution which displays the values rather than variable names in the legend as well as the relevant output values for the TA. However, unlike the default settings of addTA, the text for each output value doesn't match the colour of the line on the addTA plot. Unfortunately I haven't worked out how to get the text of the output values to match the colour of its relevant line on the addTA plot. Any suggestions?
library("quantmod")
getSymbols("YHOO")
barChart(YHOO, subset="last 4 months")
col <- c("red", "blue", "green", "orange")
temp1 <- 8
temp2 <- "SMA"
temp <- ADX(HLC(YHOO), n=temp1, maType=temp2)
legend <- rep(NA, NCOL(temp)+1)
legend[1] <- paste("ADX(HLC(YHOO)", "n=", temp1, "maType=", temp2)
for(x in 2:(NCOL(temp)+1)){
legend[x] <- (paste(colnames(temp[,(x-1)]),": ", round(last(temp[,(x-1)]),3), sep=""))
}
addTA(temp, legend = legend, col=col)
I would like to add LaTeX typesetting to elements of plots in R (e.g: the title, axis labels, annotations, etc.) using either the combination of base/lattice or with ggplot2.
Questions:
Is there a way to get LaTeX into plots using these packages, and if so, how is it done?
If not, are there additional packages needed to accomplish this.
For example, in Python matplotlib compiles LaTeX via the text.usetex packages as discussed here: http://www.scipy.org/Cookbook/Matplotlib/UsingTex
Is there a similar process by which such plots can be generated in R?
The CRAN package latex2exp contains a TeX function that translate LaTeX formulas to R's plotmath expressions. You can use it anywhere you could enter mathematical annotations, such as axis labels, legend labels, and general text.
For example:
x <- seq(0, 4, length.out=100)
alpha <- 1:5
plot(x, xlim=c(0, 4), ylim=c(0, 10),
xlab='x', ylab=TeX(r'($\alpha x^\alpha$, where $\alpha \in \{1 \ldots 5\}$)'),
type='n', main=TeX(r'(Using $\LaTeX$ for plotting in base graphics!)', bold=TRUE))
for (a in alpha) {
lines(x, a*x^a, col=a)
}
legend('topleft',
legend=TeX(sprintf(r'($\alpha = %d$)', alpha)),
lwd=1,
col=alpha)
produces this plot.
Here's an example using ggplot2:
q <- qplot(cty, hwy, data = mpg, colour = displ)
q + xlab(expression(beta +frac(miles, gallon)))
As stolen from here, the following command correctly uses LaTeX to draw the title:
plot(1, main=expression(beta[1]))
See ?plotmath for more details.
You can generate tikz code from R:
http://r-forge.r-project.org/projects/tikzdevice/
Here's something from my own Lab Reports.
tickzDevice exports tikz images for LaTeX
Note, that in certain cases "\\" becomes "\" and "$" becomes "$\" as in the following R code: "$z\\frac{a}{b}$" -> "$\z\frac{a}{b}$\"
Also xtable exports tables to latex code
The code:
library(reshape2)
library(plyr)
library(ggplot2)
library(systemfit)
library(xtable)
require(graphics)
require(tikzDevice)
setwd("~/DataFolder/")
Lab5p9 <- read.csv (file="~/DataFolder/Lab5part9.csv", comment.char="#")
AR <- subset(Lab5p9,Region == "Forward.Active")
# make sure the data names aren't already in latex format, it interferes with the ggplot ~ # tikzDecice combo
colnames(AR) <- c("$V_{BB}[V]$", "$V_{RB}[V]$" , "$V_{RC}[V]$" , "$I_B[\\mu A]$" , "IC" , "$V_{BE}[V]$" , "$V_{CE}[V]$" , "beta" , "$I_E[mA]$")
# make sure the working directory is where you want your tikz file to go
setwd("~/TexImageFolder/")
# export plot as a .tex file in the tikz format
tikz('betaplot.tex', width = 6,height = 3.5,pointsize = 12) #define plot name size and font size
#define plot margin widths
par(mar=c(3,5,3,5)) # The syntax is mar=c(bottom, left, top, right).
ggplot(AR, aes(x=IC, y=beta)) + # define data set
geom_point(colour="#000000",size=1.5) + # use points
geom_smooth(method=loess,span=2) + # use smooth
theme_bw() + # no grey background
xlab("$I_C[mA]$") + # x axis label in latex format
ylab ("$\\beta$") + # y axis label in latex format
theme(axis.title.y=element_text(angle=0)) + # rotate y axis label
theme(axis.title.x=element_text(vjust=-0.5)) + # adjust x axis label down
theme(axis.title.y=element_text(hjust=-0.5)) + # adjust y axis lable left
theme(panel.grid.major=element_line(colour="grey80", size=0.5)) +# major grid color
theme(panel.grid.minor=element_line(colour="grey95", size=0.4)) +# minor grid color
scale_x_continuous(minor_breaks=seq(0,9.5,by=0.5)) +# adjust x minor grid spacing
scale_y_continuous(minor_breaks=seq(170,185,by=0.5)) + # adjust y minor grid spacing
theme(panel.border=element_rect(colour="black",size=.75))# border color and size
dev.off() # export file and exit tikzDevice function
Here's a cool function that lets you use the plotmath functionality, but with the expressions stored as objects of the character mode. This lets you manipulate them programmatically using paste or regular expression functions. I don't use ggplot, but it should work there as well:
express <- function(char.expressions){
return(parse(text=paste(char.expressions,collapse=";")))
}
par(mar=c(6,6,1,1))
plot(0,0,xlim=sym(),ylim=sym(),xaxt="n",yaxt="n",mgp=c(4,0.2,0),
xlab="axis(1,(-9:9)/10,tick.labels,las=2,cex.axis=0.8)",
ylab="axis(2,(-9:9)/10,express(tick.labels),las=1,cex.axis=0.8)")
tick.labels <- paste("x >=",(-9:9)/10)
# this is what you get if you just use tick.labels the regular way:
axis(1,(-9:9)/10,tick.labels,las=2,cex.axis=0.8)
# but if you express() them... voila!
axis(2,(-9:9)/10,express(tick.labels),las=1,cex.axis=0.8)
I did this a few years ago by outputting to a .fig format instead of directly to a .pdf; you write the titles including the latex code and use fig2ps or fig2pdf to create the final graphic file. The setup I had to do this broke with R 2.5; if I had to do it again I'd look into tikz instead, but am including this here anyway as another potential option.
My notes on how I did it using Sweave are here: http://www.stat.umn.edu/~arendahl/computing
I just have a workaround. One may first generate an eps file, then convert it back to pgf using the tool eps2pgf. See http://www.texample.net/tikz/examples/eps2pgf/
h <- rnorm(mean = 5, sd = 1, n = 1000)
hist(h, main = expression(paste("Sampled values, ", mu, "=5, ", sigma,
"=1")))
Taken from a very help article here https://stats.idre.ucla.edu/r/codefragments/greek_letters/
You can use the following, for example:
title(sub=TeX(sprintf(paste("Some latex symbols are ", r'(\lambda)', "and", r'(\alpha)'))))
Just remember to enclose LaTeX expressions in paste() using r'()'
You can also add named objects in the paste() function. E.g.,
lambda_variable <- 3
title(sub=TeX(sprintf(paste(r'(\lambda=)', lambda_variable))))
Not sure if there are better ways to do this, but the above worked for me :)
I would like to add LaTeX typesetting to elements of plots in R (e.g: the title, axis labels, annotations, etc.) using either the combination of base/lattice or with ggplot2.
Questions:
Is there a way to get LaTeX into plots using these packages, and if so, how is it done?
If not, are there additional packages needed to accomplish this.
For example, in Python matplotlib compiles LaTeX via the text.usetex packages as discussed here: http://www.scipy.org/Cookbook/Matplotlib/UsingTex
Is there a similar process by which such plots can be generated in R?
The CRAN package latex2exp contains a TeX function that translate LaTeX formulas to R's plotmath expressions. You can use it anywhere you could enter mathematical annotations, such as axis labels, legend labels, and general text.
For example:
x <- seq(0, 4, length.out=100)
alpha <- 1:5
plot(x, xlim=c(0, 4), ylim=c(0, 10),
xlab='x', ylab=TeX(r'($\alpha x^\alpha$, where $\alpha \in \{1 \ldots 5\}$)'),
type='n', main=TeX(r'(Using $\LaTeX$ for plotting in base graphics!)', bold=TRUE))
for (a in alpha) {
lines(x, a*x^a, col=a)
}
legend('topleft',
legend=TeX(sprintf(r'($\alpha = %d$)', alpha)),
lwd=1,
col=alpha)
produces this plot.
Here's an example using ggplot2:
q <- qplot(cty, hwy, data = mpg, colour = displ)
q + xlab(expression(beta +frac(miles, gallon)))
As stolen from here, the following command correctly uses LaTeX to draw the title:
plot(1, main=expression(beta[1]))
See ?plotmath for more details.
You can generate tikz code from R:
http://r-forge.r-project.org/projects/tikzdevice/
Here's something from my own Lab Reports.
tickzDevice exports tikz images for LaTeX
Note, that in certain cases "\\" becomes "\" and "$" becomes "$\" as in the following R code: "$z\\frac{a}{b}$" -> "$\z\frac{a}{b}$\"
Also xtable exports tables to latex code
The code:
library(reshape2)
library(plyr)
library(ggplot2)
library(systemfit)
library(xtable)
require(graphics)
require(tikzDevice)
setwd("~/DataFolder/")
Lab5p9 <- read.csv (file="~/DataFolder/Lab5part9.csv", comment.char="#")
AR <- subset(Lab5p9,Region == "Forward.Active")
# make sure the data names aren't already in latex format, it interferes with the ggplot ~ # tikzDecice combo
colnames(AR) <- c("$V_{BB}[V]$", "$V_{RB}[V]$" , "$V_{RC}[V]$" , "$I_B[\\mu A]$" , "IC" , "$V_{BE}[V]$" , "$V_{CE}[V]$" , "beta" , "$I_E[mA]$")
# make sure the working directory is where you want your tikz file to go
setwd("~/TexImageFolder/")
# export plot as a .tex file in the tikz format
tikz('betaplot.tex', width = 6,height = 3.5,pointsize = 12) #define plot name size and font size
#define plot margin widths
par(mar=c(3,5,3,5)) # The syntax is mar=c(bottom, left, top, right).
ggplot(AR, aes(x=IC, y=beta)) + # define data set
geom_point(colour="#000000",size=1.5) + # use points
geom_smooth(method=loess,span=2) + # use smooth
theme_bw() + # no grey background
xlab("$I_C[mA]$") + # x axis label in latex format
ylab ("$\\beta$") + # y axis label in latex format
theme(axis.title.y=element_text(angle=0)) + # rotate y axis label
theme(axis.title.x=element_text(vjust=-0.5)) + # adjust x axis label down
theme(axis.title.y=element_text(hjust=-0.5)) + # adjust y axis lable left
theme(panel.grid.major=element_line(colour="grey80", size=0.5)) +# major grid color
theme(panel.grid.minor=element_line(colour="grey95", size=0.4)) +# minor grid color
scale_x_continuous(minor_breaks=seq(0,9.5,by=0.5)) +# adjust x minor grid spacing
scale_y_continuous(minor_breaks=seq(170,185,by=0.5)) + # adjust y minor grid spacing
theme(panel.border=element_rect(colour="black",size=.75))# border color and size
dev.off() # export file and exit tikzDevice function
Here's a cool function that lets you use the plotmath functionality, but with the expressions stored as objects of the character mode. This lets you manipulate them programmatically using paste or regular expression functions. I don't use ggplot, but it should work there as well:
express <- function(char.expressions){
return(parse(text=paste(char.expressions,collapse=";")))
}
par(mar=c(6,6,1,1))
plot(0,0,xlim=sym(),ylim=sym(),xaxt="n",yaxt="n",mgp=c(4,0.2,0),
xlab="axis(1,(-9:9)/10,tick.labels,las=2,cex.axis=0.8)",
ylab="axis(2,(-9:9)/10,express(tick.labels),las=1,cex.axis=0.8)")
tick.labels <- paste("x >=",(-9:9)/10)
# this is what you get if you just use tick.labels the regular way:
axis(1,(-9:9)/10,tick.labels,las=2,cex.axis=0.8)
# but if you express() them... voila!
axis(2,(-9:9)/10,express(tick.labels),las=1,cex.axis=0.8)
I did this a few years ago by outputting to a .fig format instead of directly to a .pdf; you write the titles including the latex code and use fig2ps or fig2pdf to create the final graphic file. The setup I had to do this broke with R 2.5; if I had to do it again I'd look into tikz instead, but am including this here anyway as another potential option.
My notes on how I did it using Sweave are here: http://www.stat.umn.edu/~arendahl/computing
I just have a workaround. One may first generate an eps file, then convert it back to pgf using the tool eps2pgf. See http://www.texample.net/tikz/examples/eps2pgf/
h <- rnorm(mean = 5, sd = 1, n = 1000)
hist(h, main = expression(paste("Sampled values, ", mu, "=5, ", sigma,
"=1")))
Taken from a very help article here https://stats.idre.ucla.edu/r/codefragments/greek_letters/
You can use the following, for example:
title(sub=TeX(sprintf(paste("Some latex symbols are ", r'(\lambda)', "and", r'(\alpha)'))))
Just remember to enclose LaTeX expressions in paste() using r'()'
You can also add named objects in the paste() function. E.g.,
lambda_variable <- 3
title(sub=TeX(sprintf(paste(r'(\lambda=)', lambda_variable))))
Not sure if there are better ways to do this, but the above worked for me :)