I want to add a greek character to the x-axis of my histogram plot in R.
I can write the greek character alone or with the hat, but the problem is that I need this character to be come with a hat and asterisk () together. More specifically, I want the something like hat(phi^). Here is what I have done:
x = rnorm(1000)
hist( x, nclass = 100, cex.lab=1.5, xlab = expression(hat(phi^*)),
ylab="Frequency", main="", cex.axis=1.5 )
Thanks.
What about using ggplot2 instead of base R. You can then use latex2exp::TeX to use (some) LaTeX expressions in the axes labels.
set.seed(2018)
x = rnorm(1000)
library(ggplot2)
library(latex2exp)
ggplot(data.frame(x = x), aes(x)) +
geom_histogram(bins = 100) +
theme_minimal() +
xlab(TeX("$\\widehat{\\phi^*}$"))
You need to escape the backslashes with an extra backslash and wrap math expressions inside $ delimiters (just as in regular LaTeX inline math). I used \widehat{}, but you can also use hat{} instead.
Here is the best looking solution that I found:
hist( x, nclass = 100, cex.lab=1.5, xlab = expression(hat(phi)~"*"),
ylab="Frequency", main="", cex.axis=1.5 )
To get the star under the hat, I don't know of any nice looking solution with base plot functions. I think #Maurits Evers' method is the best compromise between complexity and prettiness of the result.
But here is anyway a more "advanced" (and maybe a little bit over the top, but well...) solution. It is based on this blog post: http://iltabiai.github.io/tips/latex/2015/09/15/latex-tikzdevice-r.html
To make it work, you will need to install the tikzDevice package.
First, load the packages and create the data-set.
library(tikzDevice)
library(ggplot2)
dat <- data.frame(x = rnorm(1000))
Then create a TeX file that will contain the "translation" of your R plot in "tikz" language.
tikz(file = "plot_test.tex", width = 5, height = 5, standAlone = TRUE)
ggplot(dat, aes(x = x)) +
geom_histogram(color="white") + theme_bw() +
labs( x = "$\\widehat{\\phi^*}$")
dev.off()
Then, you can either directly copy or call the LaTeX code into your own LaTeX document (then the standAlone=TRUE argument is not necessary), or you can use these two very useful function to generate a pdf version and see the result.
tools::texi2dvi("plot_test.tex", pdf=TRUE)
system(paste(getOption('pdfviewer'), "plot_test.pdf"))
Related
I'm new to flowCore + R. I would like to mimic a histogram plot after gating that can be manually done in FlowJo software. I got something similar but it doesn't look quite right because it is a "density" plot and is shifted. How can I get the x axis to shift over and look similar to how FlowJo outputs the plot? I tried reading this document but couldn't find a plot similar to the one in FlowJo: howtoflowcore Appreciate any guidance. Thanks.
code snippet:
library(flowCore)
parentpath <- "/parent/path"
subfolder <- "Sample 1"
fcs_files <- list.files(paste0(parentpath, subfolder), pattern = ".fcs")
fs <- read.flowSet(fcs_files)
rect.g <- rectangleGate(filterId = "main",list("FSC-A" = c(1e5, 2e5), "SSC-A" = c(3e4,1e5)))
fs_sub <- Subset(fs, rect.g)
p <- ggcyto(fs_sub[[15]], aes(x= `UV-379-A`)) +
geom_density(fill='black', alpha = 0.4) +
ggcyto_par_set(limits = list(x = c(-1e3, 5e4), y = c(0, 6e-5)))
p
FlowJo output:
R FlowCore output:
The reason that for the "shift" is that the x axis is logarithmic (base 10) in the flowJo graph. To achieve the same result in R, add
+ scale_x_log10()
after the existing code. This might interact weirdly with the axis limits you've set, so bare that in mind.
To make the y-axis "count" rather than density, you can change the first line of your ggcyto() call to:
aes(x= `UV-379-A`, y = after_stat(count))
Let me know if that works - I don't have your data to hand so that's all from memory!
For any purely aesthetic changes, they are relatively easy to look up.
I want to subscript the '2' in 'NO2' in the main heading and the xlabel, and I want to add '(µg/m3)' (with a superscript '3') in the xlabel, but the way I did it before for histograms doesn't work. Any help would be gratefully received!
This is what I have so far:
library(ggpubr)
ggdensity(bgbind$no2,
main = "Density plot of background NO2 concentrations",
xlab = "NO2")
You can just use the symbols directly:
ggdensity(bgbind$no2,
main = "Density plot of background NO₂ concentrations",
xlab = "NO₂ (µg/m³)")
A somewhat more portable way of doing this is using unicode escape sequences. I tend to do this by looking up, say, "unicode subscript 2" in a web search engine. This will usually give you the result in the format "U+AAAA" where "AAAA" is a four digit hexadecimal number. If you do "\uAAAA" as a string in R, this will be converted to the appropriate unicode symbol. So, for example, look at what prints in the console here:
"NO\u2082 (\u03BCg/m\u00bB)"
#> [1] "NO₂ (μg/m»)"
You can use bquote().
Here is an example with ggplot2:
library(ggplot2)
bgbind <- data.frame(
no2 = 1:10,
y = 1:10
)
ggplot(bgbind, aes(no2, y)) +
geom_point() +
labs(title = bquote("Density plot of background NO"[2] ~ "concentrations"),
x = bquote(NO[2] ~ (mu*g/m^3)))
Assuming that, by main, you meant the title of the plot.
I cannot test it as I don't have your dataset and I am unable to install the package ggpubr for some reason, but in your situation, this should work:
library(ggpubr)
ggdensity(bgbind$no2,
main = bquote("Density plot of background NO"[2] ~ "concentrations"),
xlab = bquote(NO[2] ~ (mu*g/m^3)))
Inside bquote(), [] subscripts what is inside, ^ superscripts what follows, ~ adds a space, mu is turned into the symbol micro, * juxtaposes 2 elements.
I would like to add LaTeX typesetting to elements of plots in R (e.g: the title, axis labels, annotations, etc.) using either the combination of base/lattice or with ggplot2.
Questions:
Is there a way to get LaTeX into plots using these packages, and if so, how is it done?
If not, are there additional packages needed to accomplish this.
For example, in Python matplotlib compiles LaTeX via the text.usetex packages as discussed here: http://www.scipy.org/Cookbook/Matplotlib/UsingTex
Is there a similar process by which such plots can be generated in R?
The CRAN package latex2exp contains a TeX function that translate LaTeX formulas to R's plotmath expressions. You can use it anywhere you could enter mathematical annotations, such as axis labels, legend labels, and general text.
For example:
x <- seq(0, 4, length.out=100)
alpha <- 1:5
plot(x, xlim=c(0, 4), ylim=c(0, 10),
xlab='x', ylab=TeX(r'($\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'm trying to generate a beautiful legend in R plots. I have a factor=1e-5, that should appear nicely formatted in the legend. I found a nice function in the package sfsmisc, that transforms numbers to expressions. To add this expression to my bquote command, it seems that I need to transform itto a call. unfortunately, there are braces added at the end of the string (10^-5()).
Is there a way to avoid the addition of thoses braces? Or is there even an easier way to transform numbers to plotmaths commands for their use in legends? (without doing it manually)
factor = 1e-5
alpha = 1:10
omega = alpha^2 * factor
plot (
alpha
, omega
, xlab=bquote(alpha)
, ylab=bquote(omega)
, type="b"
)
text = expression()
# standard version
text[1] = as.expression(bquote(alpha%*%.(factor)))
# beautified version (use pretty10exp from sfsmisc package!?)
library("sfsmisc")
pretty = as.call(pretty10exp(factor, drop.1=T))
text[1] = as.expression(bquote(alpha^2%*%.(pretty)))
# add legend
legend("topleft", legend=text, pch=1, lty=1)
Here's what you can do instead with function parse:
text <- paste("alpha^2%*%",parse(text=pretty10exp(factor,drop.1=T)),sep="")
text
[1] "alpha^2%*%10^-5" # which we then use as the expression in your call to legend
legend("topleft", legend=parse(text=text), pch=1, lty=1)
See ?parse for more explanation on how this work.
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 :)