I am fairly new to R/ggplot2 and still learning on the go. Hopefully I am not missing something obvious!
I am trying to create several different plots using ggplot2 that I am layouting using the function plot_grid from the cowplot package to make the plots visible side by side and add plot numeration and captions. The problem is that if the generated plots are displayed in a small window or I have many plots beside one another then the titles of the two plots sometimes overlap. To solve this problem I tried to automatically insert line breaks in my too long titles using code I found in another thread since I wanted the text size of the titles to stay constant.
Using the following code I can easily automatically insert the necessary line breaks to make my title a specific width, but the problem is that I always need to enter a numeric value for the width. Depending on the number of plots I am inserting this value would of course change. I could of course go through my code and manually set the width for each set of plots until it is the correct value, but I was hoping to automate this process so that the title width is adjusted automatically to match the width of the x-axis. Is there anyway to implement this in R?
#automatically line break and add titles
myplot_theme1 = function (plot, x.title = NULL, y.title = NULL, plot.title = NULL) {
plot +
labs(title = paste(strwrap(plot.title, width = 50), collapse = "\n"),
x = x.title,
y = y.title)
}
# generate an example plot
data_plot <- data.frame(x = rnorm(1000), y = rnorm (1000))
plot1 <- ggplot(data_plot, aes(x = x, y = y)) + geom_point()
title <- "This is a title that is very long and does not display nicely"
myplot_theme1(plot1, plot.title = title)
My test plot
I have tried searching but I haven't found any solutions that seem to address what I am looking for. The only solution I did find that looked promising was based on the package gridDebug. This packages doesn't seem to be supported by my operating system anymore though (macOS Sierra Version 10.12.6) since when I try to install it I get the following error message:
Warning in install.packages: dependencies ‘graph’, ‘Rgraphviz’ are not available
And on the CRAN package documentation it states that the package is not even available for macOS El Capitan which was my previous operating system. If someone knows what is causing this issue so that I could try the solution from the above thread that would of course be great as well.
One idea (but perhaps not an ideal solution) is to adjust the size of text based on the number of characters in the title. You can adjust ggplot properties using theme and in this case you want to adjust plot.title (the theme property, not your variable). plot.title has elements size and horizontal justification hjust, the latter is in range [0,1].
# generate an example plot
data_plot <- data.frame(x = rnorm(1000), y = rnorm (1000))
plot1 <- ggplot(data_plot, aes(x = x, y = y)) + geom_point()
title1 <- "This is a title that is very long and does not display nicely"
title2 <- "I'm an even longer sentence just test me out and see if I display the way you want or you'll be sorry"
myplot_theme1 = function (plot, x.title = NULL, y.title = NULL, plot.title = NULL) {
plot +
labs(title = plot.title,
x = x.title,
y = y.title) +
theme(plot.title = element_text(size=800/nchar(plot.title), hjust=0.5)) # 800 is arbitrarily chosen
}
myplot_theme1(plot1, plot.title = title1)
myplot_theme1(plot1, plot.title = title2)
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.
Is there a way to force an automatic line break in the ggtitle command?
As part of a shiny application I use different plots with an input variable for the title.
Unfortunately, some of these variable values are too long to be displayed.
I came across one possibility by inserting \n (or a line break) manually in advance (Details here: Improve editing of multiline title in ggplot that uses \n and extends far to the right). There, something like ggtitle(paste("", title, "", sep = "\n")) would be suggested.
Since including \n would be error prone as well as not flexible for different plot sizes I´m looking for another possibility.
Here is an minimal working example (adapted from lawyeR question linked above):
DF <- data.frame(x = rnorm(400))
title_example <- "This is a very long title describing the plot in its details. The title should be fitted to a graph, which is itself not restricted by its size."
plot <- ggplot(DF, aes(x = x)) + geom_histogram() +
ggtitle(title_example)
You can find a image here: https://i.stack.imgur.com/6MMKF.jpg
Do you have an idea how to e.g. adapt the sep = operator to break lines automatically or are there maybe packages/ workarounds? Thanks!
The ggtext package's text elements could help solve this. element_textbox_simple() automatically wraps the text inside. Try resizing the graphics device window, it adapts!
library(ggplot2)
library(ggtext)
DF <- data.frame(x = rnorm(400))
title_example <- "This is a very long title describing the plot in its details. The title should be fitted to a graph, which is itself not restricted by its size."
ggplot(DF, aes(x = x)) + geom_histogram() +
ggtitle(title_example) +
theme(plot.title = element_textbox_simple())
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
I am trying to change text label sizes inside my plot (not the axes, rather the label annotations)
I am working with a phyloseq object but I don't think that matters.
Here is the code and the output. Any suggestions?
plot_ordination(prokaryote_ra, ordBC, color = "Stage", label="SampleID") + ggtitle("PCoA: Bray-Curtis")
graph of ordination plot with label annotations that are too small
Looks like size for the text label is a fixed value 2, in the plot_ordination() function see L1135 at GitHub in plot-methods.R file
...
p = p + geom_text(label_map, data=rm.na.phyloseq(DF, label),
size=2, vjust=1.5, na.rm=TRUE) # <--- here size is set to 2
...
Solution would be either submit an issue at GitHub, and wait for an update from maintainer, or copy paste the function locally, and change the size to match your needs.
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've been trying to draw two plots using R's ggplot library in RStudio. Problem is, when I draw two within one function, only the last one displays (in RStudio's "plots" view) and the first one disappears. Even worse, when I run ggsave() after each plot - which saves them to a file - neither of them appear (but the files save as expected). However, I want to view what I've saved in the plots as I was able to before.
Is there a way I can both display what I'll be plotting in RStudio's plots view and also save them? Moreover, when the plots are not being saved, why does the display problem happen when there's more than one plot? (i.e. why does it show the last one but not the ones before?)
The code with the plotting parts are below. I've removed some parts because they seem unnecessary (but can add them if they are indeed relevant).
HHIplot = ggplot(pergame)
# some ggplot geoms and misc. here
ggsave(paste("HHI Index of all games,",year,"Finals.png"),
path = plotpath, width = 6, height = 4)
HHIAvePlot = ggplot(AveHHI, aes(x = AveHHI$n_brokers))
# some ggplot geoms and misc. here
ggsave(paste("Average HHI Index of all games,",year,"Finals.png"),
path = plotpath, width = 6, height = 4)
I've already taken a look here and here but neither have helped. Adding a print(HHIplot) or print(HHIAvePlot) after the ggsave() lines has not displayed the plot.
Many thanks in advance.
Update 1: The solution suggested below didn't work, although it works for the answer's sample code. I passed the ggplot objects to .Globalenv and print() gives me an empty gray box on the plot area (which I imagine is an empty ggplot object with no layers). I think the issue might lie in some of the layers or manipulators I have used, so I've brought the full code for one ggplot object below. Any thoughts? (Note: I've tried putting the assign() line in all possible locations in relation to ggsave() and ggplot().)
HHIplot = ggplot(pergame)
HHIplot +
geom_point(aes(x = pergame$n_brokers, y = pergame$HHI)) +
scale_y_continuous(limits = c(0,10000)) +
scale_x_discrete(breaks = gameSizes) +
labs(title = paste("HHI Index of all games,",year,"Finals"),
x = "Game Size", y = "Herfindahl-Hirschman Index") +
theme(text = element_text(size=15),axis.text.x = element_text(angle = 0, hjust = 1))
assign("HHIplot",HHIplot, envir = .GlobalEnv)
ggsave(paste("HHI Index of all games,",year,"Finals.png"),
path = plotpath, width = 6, height = 4)
I'll preface this by saying that the following is bad practice. It's considered bad practice to break a programming language's scoping rules for something as trivial as this, but here's how it's done anyway.
So within the body of your function you'll create both plots and put them into variables. Then you'll use ggsave() to write them out. Finally, you'll use assign() to push the variables to the global scope.
library(ggplot2)
myFun <- function() {
#some sample data that you should be passing into the function via arguments
df <- data.frame(x=1:10, y1=1:10, y2=10:1)
p1 <- ggplot(df, aes(x=x, y=y1))+geom_point()
p2 <- ggplot(df, aes(x=x, y=y2))+geom_point()
ggsave('p1.jpg', p1)
ggsave('p2.jpg', p2)
assign('p1', p1, envir=.GlobalEnv)
assign('p2', p2, envir=.GlobalEnv)
return()
}
Now, when you run myFun() it will write out your two plots to .jpg files, and also drop the plots into your global environment so that you can just run p1 or p2 on the console and they'll appear in RStudio's Plot pane.
ONCE AGAIN, THIS IS BAD PRACTICE
Good practice would be to not worry about the fact that they're not popping up in RStudio. They wrote out to files, and you know they did, so go look at them there.