When I render a boxplot on a PDF device in R there is a large white space besides the graph, especially at the top that i intent to reduce.
My script is basically just:
data <- read.csv("input.csv")
pdf(file="output.pdf", width=4, height=5)
boxplot(data, xlab="input graphs", ylab="vertex count")
This leads to something like:
where the grey outline indicates the end of the document.
I tried to use the par attributes "mar" and "mai" as described in https://stat.ethz.ch/R-manual/R-devel/library/graphics/html/par.html but it had no effect.
boxplot(data, mar=c(0,0,0,0=, mai=c(0,0,0,0))
Do you have an advice how I can gain whitespace control? I want to have zero outer whitespace as the generated graph will be used in a Latex environment that provides sufficient spacings on its own. I am using Ubuntu as OS.
Define mar right after pdf. Try this as an example
pdf(file = "test.pdf", width = 5, height = 5)
par(mar = c(5, 5, 0.05, 0.05))
set.seed(42)
plot(rnorm(20))
dev.off()
Related
I'm trying to do a forest plot using metafor::forest. The problem is that because I have over 100 studies the output is unreadable because the rows blend together and overlap unless I choose a very small font (in which case you also can't read it).
Any ideas on how to plot this so that the font is large enough to be read without having all rows overlap?
Here's the code I'm using:
library(metafor)
res <- rma(yi, vi, data=dat)
par(mar = c(6, 6, 6, 6))
forest(res, addpred=T, header=TRUE, atransf=exp, at=log(c(.05, 0.5, 5, 15)), xlim=c(-5,5), ylim=c(-3,190), cex=.75)
This is the output
The only way it doesn't overlap is with cex = .05, but it is of course impossible to see anything:
I do not known the library nor the data, and cannot reproduce your example, but, for case, try using another output device:
png("file.png" , width = 480, height = 4000)
plot(runif(100))
dev.off()
Then see result file in current (getwd()) directory.
I am trying to draw a standard triangular mediation diagram using DiagrammeR in R (it can also interpret graphviz code). On the whole, it's working fine but the edge label text gets placed oddly. The bottom edge label is not centered and the two angled edge labels are positioned at different heights (see the red lines in the diagram below). Is there a way to manually assign positions to edge text or get something more consistent?`
library(DiagrammeR)
# Create a node data frame (ndf)
ndf <- create_node_df(
n = 3,
label = c("Experimental\nTreatment", "Some\nMediator", "Outcome\nof Interest"),
shape = rep("rectangle", 3),
style = "empty",
fontsize = 6,
fixedsize = TRUE,
height = .5,
width = .75,
color = "gray40",
x = c(1, 2, 3),
y = c(1, 2, 1)
)
# Create an edge data frame (edf)
edf <- create_edge_df(
from = c(1, 1, 2),
to = c(2, 3, 3),
label = c("1.1*", "2.0*", "-0.33***"),
fontsize = 6,
minlen = 1,
color = "gray40",
)
# Create a graph with the ndf and edf
graph <- create_graph(
nodes_df = ndf,
edges_df = edf
)
graph %>%
render_graph()
I would also love to know the answer to this.
I have tried to delete the default "layout" graph attribute and set direction of graph layout via:
graphAttr <- DiagrammeR::get_global_graph_attrs(graph)
But, I get the following error:
Error: 'get_global_graph_attrs' is not an exported object from 'namespace:DiagrammeR'
....which it is, consequently, I am stuck.
After fiddling with DiagrammeR for a while, I ended up switching to the LaTeX diagramming package TikZ. It allows for enormous control of every aspect of the diagram but can be overwhelming. TikZ would require a bit of tweaking, also, to get diagrams into HTML output if that's important. For a presentation using LaTeX's Beamer class for slides, generating TikZ code with a function in R worked well. That TikZ code was then written to a text file that could be imported automatically via the LaTeX command \input{path/to/file.txt} or just copied and pasted into my slides.
See the code for two DiagrammeR solutions and the TikZ solution, here: https://stackoverflow.com/a/64886536/893399
I build scatterplots using ggplot2 in R. I then want to save them as svg files with Cairo::CairoSVG. It seems to work fine except for the point size, which is enlarged in the resulting .svg file.
Here comes some example code:
library (ggplot2)
my_plot <- ggplot(mpg, aes(cty, hwy)) +
geom_point(size = 0.5)
x11 (width = 6, height = 6)
my_plot
Cairo::CairoSVG (file = "my_path",
width = 6, height = 6)
print (my_plot)
dev.off()
And this is what I get: on the right hand, the plot printed in R and on the left side the saved .svg-file opened in Inkscape. It looks fine except for the point size, which is a pity. Are there any ideas on how to get the right point-size? I tried different point sizes and also shapes, with similarly unmatched results.
Note that I seek to stick with Cairo::CairoSVG, beacuse in the final plots I wish to use custom fonts which are printed nicely with Cairo::CairoSVG. Any help is appreciated.
EDIT: I am working on a Windows machine.
Preliminary remark: when you pass width = 6, height = 6 in the Cairo::CairoSVG() parameters, you provide potentially different parameters (resolution and display) from the ones used in the RStudio plot panel.
To get the exact same image than the one rendered in the panel as well as using Cairo, you can use this alternative (dev.size('px') returns the dimensions of the current plot panel):
library (ggplot2)
my_plot <- ggplot(mpg, aes(cty, hwy)) +
geom_point(size = 0.5)
my_plot
mirror <- recordPlot()
png(filename = "mypath",
width = dev.size('px')[1]/96,
height = dev.size('px')[2]/96,
res = 96, # base RStudio resolution
units = "in",
type = "cairo") # calls CairoSVG
replayPlot(mirror)
dev.off()
(Note : I prefer the use of png() rather than ggsave() because it will save the entire last plot. I have observed that ggsave() would save only the last facet of a grid, for example)
I'm trying to output a Stem and Leaf plot in R as an image. I'm not sure if there's a nice library which can accomplish this but below is some of the code I've tried.
jpeg(filename="stem.jpeg",width=480,height=480, units="px",pointsize=12)
plot.new()
tmp <- capture.output(stem(men, scale = 1, width = 40))
text( 0,1, paste(tmp, collapse='\n'), adj=c(0,1), family='mono' )
dev.off()
This above code resulted in the data being saved, but it looks very blurry and the plot gets cut off pretty badly. When adding a histogram to an image, R seems to do a good job to scale everything to fit in the size of the image.
jpeg(filename="stem.jpeg",width=480,height=480,
units="px",pointsize=12)
stem(men, scale = 1, width = 40)
dev.off()
This created the image but had no content within it.
Any ideas? Thanks!
That's because stem and leaf plots produce text not images. You can save the text as follows using the sink command: http://stat.ethz.ch/R-manual/R-devel/library/base/html/sink.html
sink(file=“Stem.txt”)
stem(men, scale = 1, width = 40)
sink(file=NULL)
unlink("stem.txt")
To export a stemplot as graphics, you can use a vector graphics format, such
as .eps, .pdf, or .emf. For example, a windows metafile:
win.metafile("stem.wmf", pointsize = 10)
plot.new()
tmp <- capture.output(stem(mtcars$mpg))
text(0,1,paste(tmp,collapse='\n'),family='mono',adj=c(0,1))
dev.off()
(I'm still learning how to handle images in R; this is sort of a continuation of rpart package: Save Decision Tree to PNG )
I'm trying to save a decision tree plot from rpart in PNG form, instead of the provided postscript. My code looks like this:
png("tree.png", width=1000, height=800, antialias="cleartype")
plot(fit, uniform=TRUE,
main="Classification Tree")
text(fit, use.n=TRUE, all=TRUE, cex=.8)
dev.off()
but cuts off a little of the labels for the edge nodes on both sides. this isn't a problem in the original post image, which I've converted to png just to check. I've tried using both oma and mar settings in par, which were recommended as solutions for label/text problems, and both added white space around the image but don't show anymore of the labels. Is there any way to get the text to fit?
The rpart.plot package plots rpart trees and automatically takes care of
the margin and related issues. Use rpart.plot (instead of plot and text in the rpart package). For example:
library(rpart.plot)
data(ptitanic)
fit <- rpart(survived~., data=ptitanic)
png("tree.png", width=1000, height=800, antialias="cleartype")
rpart.plot(fit, main="Classification Tree")
dev.off()
The default margin is 0. So if your text is a set of words or just a long word, try to put more margin in plot call. For example,
plot(fit, uniform=TRUE,margin=0.2)
text(fit, use.n=TRUE, all=TRUE, cex=.8)
Alternatively, you can adjust text font size by changing cex in text call. For example,
plot(fit, uniform=TRUE)
text(fit,use.n=TRUE, all=TRUE, cex=.7)
Of course, you can adjust both mar in plot call and cex in text call to get what you want.
On rpart man, at rpart() examples the author gives the solution, set par options with xpd = NA:
par(mfrow = c(1,2), xpd = NA)
otherwise on some devices the text is clipped
Problem tiwh titanic dataset is rplot will not join ages and fare to display a nive "age > 10" label. It will display them by extension, like:
age = 11,18,19,22,24,28,29,30,32,33,37,39,40,42,45.5,5,56,58,60...
That makes no room for labels (see the picture)
bad labels
Solution is here:
https://community.rstudio.com/t/rpart-result-is-too-small-to-see/60702/4
Basically, you have to mutate age and fare columns into numeric variables. Like:
clean_titanic <- titanic %>%
select(-c(home.dest, cabin, name, x, ticket)) %>%
mutate(
pclass = factor(pclass, levels = c(1, 2, 3), labels = c('Upper', 'Middle', 'Lower')),
survived = factor(survived, levels = c(0, 1), labels = c('No', 'Yes')),
# HERE. Also notice I'm removing dots from numbers
age = as.numeric(age),
fare = as.numeric(fare)
)
That will give you better labels, and room for them in the plot.
One more thing: you could get a warning when you force non numeric values with as.numeric, and there are a couple of ways to solve that, like replacing characters or ignoring the warning. Ignore like:
suppressWarnings(as.numeric(age)))
good plot