I would like to place two (somewhat non-standard) grid graphics in a single plot in R.
Try:
require(vcd)
mosaic(Titanic)
assoc(Titanic)
The trouble is that these aren't lattice graphics, and to my knowledge do not come with a layout argument or similar. And since these are grid graphs, they're impervious to base graph tricks like par(mfrow=c(1,2)).
How can I place the two graphs above in a single plot, with both graphs on the same line?
I already tried the suggestions in How to plot grid plots on a same page?, but they don't seem to work for vcd plots. Ultimately I would like to obtain something similar to:
Neither plot seems to return any object and I cant see how to grab the grobs from looking at grid.ls(). So using the idea from this answer
library(vcd)
library(gridGraphics)
library(gridExtra)
mosaic(Titanic)
m <- grid.grab()
assoc(Titanic)
a <- grid.grab()
grid.newpage()
grid.arrange(m, a, ncol=2)
Im sure there will be a more grid-like approach but ...
Something similar to the solution in How to plot grid plots on a same page? can also be used for vcd displays. The difference is that you need to set newpage = FALSE (to prevent opening a new display) and you need to push and pop the viewport yourself (which can be handy when re-using vcd graphics in more complicated displays such as partykit trees).
The mosaic and association display for the Titanic data can be visualized as:
grid.newpage()
pushViewport(viewport(layout = grid.layout(1, 2)))
pushViewport(viewport(layout.pos.col = 1, layout.pos.row = 1))
mosaic(Titanic, newpage = FALSE)
popViewport()
pushViewport(viewport(layout.pos.row = 1, layout.pos.col = 2))
assoc(Titanic, newpage = FALSE)
popViewport()
yielding
Another option is vcd’s mplot() function (for details, see ?vcd::mplot):
library(vcd)
mplot(
mosaic(Titanic, return_grob = TRUE),
assoc(Titanic, return_grob = TRUE),
keep_aspect_ratio = FALSE
)
Related
I am trying to create and record plots in a 1x1 device:
par(mfrow = c(1, 1) )
plot(rnorm(10) )
p1 <- recordPlot()
plot(rnorm(20) )
p2 <- recordPlot()
and then to put them in a new layout (e.g., a 1x2 device):
par(mfrow = c(1, 2) )
p1
p2
However, this produce the same effect (i.e., plotting each plot in a 1x1 device). It seems replaying plots uses the original layout (graphical parameters) that was in effect when they were recorded.
Is there some method that allows a saved plot to be replayed in a new layout ?
NB: I am aware this would be easier via ggplot2, but my question is about base plots.
I did some digging, and I don't think this is possible. I used the following to look at what attributes are available inside the object. None of them seemed to indicate the layout could be adjusted.
summary(p1)
p1[[1]]
p1[[2]]
If you need the same plot across two different layouts could you use set.seed() to recreated the same plot? See the example below.
par(mfrow = c(1, 1))
set.seed(1234)
plot(rnorm(10))
par(mfrow = c(1, 2))
set.seed(1234)
plot(rnorm(10))
I'd be interested to see if anyone else has a better answer!
I'm trying to arrange a phylogenetic tree onto a graph showing physiological data for a set of related organisms. Something like the picture below. This was put together in powerpoint from 2 separate graphs. I guess it gets the job done, but I was hoping to create a single image which I think will be easier to format into a document. I am able to produce the graph I want using ggplot2, and import the tree using ape. I was thinking there should be a way to save the tree as a graphical object and then arrange it with the graph using the gridarrange function in gridExtra. The problem is that ape won't let me save the tree as a graphical object, e.g.,
p2<-plot(tree, dir = "u", show.tip.label = FALSE)
just plots the tree and when you call p2 it just gives a list of arguments. I'm wondering if anyone has any tips.
Thanks!
I'm not sure if that will work with gtable from CRAN
require(ggplot2)
require(gridBase)
require(gtable)
p <- qplot(1,1)
g <- ggplotGrob(p)
g <- gtable_add_rows(g, unit(2,"in"), nrow(g))
g <- gtable_add_grob(g, rectGrob(),
t = 7, l=4, b=7, r=4)
grid.newpage()
grid.draw(g)
#grid.force()
#grid.ls(grobs=F, viewports=T)
seekViewport("layout.7-4-7-4")
par(plt=gridPLT(), new=TRUE)
plot(rtree(10), "c", FALSE, direction = "u")
upViewport()
first I'd like to thanks baptiste for ALL his multiple answers that solved most of my issues with ggplot2.
second, I had a similar question which was to include a tree from ape inside a heatmap obtained with ggplot2. Baptiste made my day, and though my simplified version could help.
I used only what was useful for me (removing the addition of gg_rows).
library(ape)
tr <- read.tree("mytree.tree")
# heat is the heatmap ggplot, using geom_tile
g <- ggplotGrob(heat)
grid.newpage()
grid.draw(g)
# use oma to reduce the tree so it fits
par(new = TRUE, oma = c(5, 4, 5, 38))
plot(tr)
nodelabels(tr$node.label, cex = 1, frame = "none", col = "black", adj = c(-0.3, 0.5))
add.scale.bar()
# use dev.copy2pdf and not ggsave
dev.copy2pdf(file = "heatmap_prob.pdf")
the result is here
i am trying to display two or more heatmaps side by side in the same png or pdf . The layout or mfcol is not working in the case. Can someone please help me out with this.
Here's one option using the recently introduced gridGraphics package,
library(gridGraphics)
library(grid)
heatmap(as.matrix(mtcars))
library(gridGraphics)
grab_grob <- function(){
grid.echo()
grid.grab()
}
g <- grab_grob()
grid.newpage()
# library(gridExtra)
# grid.arrange(g,g, ncol=2, clip=TRUE)
lay <- grid.layout(nrow = 1, ncol=2)
pushViewport(viewport(layout = lay))
grid.draw(editGrob(g, vp=viewport(layout.pos.row = 1,
layout.pos.col = 1, clip=TRUE)))
grid.draw(editGrob(g, vp=viewport(layout.pos.row = 1,
layout.pos.col = 2, clip=TRUE)))
upViewport(1)
As stated in the help document for heatmap.2,
'heatmap.2()' uses 'layout' and draws the 'image' in the lower
right corner of a 2x2 layout. Consequentially, it can not be
used in a multi column/row layout, i.e., when 'par(mfrow= *)' or
'(mfcol= *)' has been called.
The same is true for heatmap.
Here's a way of doing that. It is very hacky but I think that when a function doesn't do what you want to do the best solution is to make it do it anyway.
Function heatmap.2 contains the following three lines at mid-way through its code:
...
op <- par(no.readonly = TRUE)
on.exit(par(op))
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
...
It is because of them that you can't use layout and par(mar=...) since it overrides it.
Copy the code of heatmap.2 into a new function (say heatmap.3) and remove those three lines:
heatmap.3 <- function(... #etc etc with the exact same code minus those 3 lines
Then your code to produce your two heatmaps side by side will be, for instance:
layout(rbind(c(4,3,8,7),c(2,1,6,5)),
widths = c(1,2,1,2), heights = c(1,2), respect = FALSE)
heatmap.3(x)
heatmap.3(y)
When preparing your layout remember that the heatmap code plot first the heatmap itself, then the "row" dendrogram, then the "col" dendrogram and finally the histogram, hence the order from top to bottom, left to right is 4, 3, 2, 1 meaning when both heatmap are side by side it becomes 4, 3, 8, 7, 2, 1, 6, 5.
After having exactly the same problem, I came up with the following solution:
1) Use ggplot2 to make your heatmap with dendrogram like here: Reproducing lattice dendrogram graph with ggplot2 and then arrange it with multiplot() function (http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_%28ggplot2%29/)
2) However, this is a lot of work and I wanted to stick with the base heatmap() function. The following is easy (though not plain R) and works on Linux if you have imagemagick installed:
m <- matrix(runif(10^2), ncol=10)
for (i1 in 1:4) {
ifile <- paste0(i1,'_heatmap.pdf')
pdf(ifile)
heatmap(m)
d <- dev.off()
}
system('montage -geometry 100% -tile 2x2 ./*_heatmap.pdf outfile.pdf')
Is there a way to put the plot generated by plot function and the plot by ggplot function in R in one page side-by-side?
It is easy to put plots created by the same function into one page using par or multiplot function, but I can't figure out the above question.
You can do this using the gridBase package and viewPorts.
library(grid)
library(gridBase)
library(ggplot2)
# start new page
plot.new()
# setup layout
gl <- grid.layout(nrow=1, ncol=2)
# grid.show.layout(gl)
# setup viewports
vp.1 <- viewport(layout.pos.col=1, layout.pos.row=1)
vp.2 <- viewport(layout.pos.col=2, layout.pos.row=1)
# init layout
pushViewport(viewport(layout=gl))
# access the first position
pushViewport(vp.1)
# start new base graphics in first viewport
par(new=TRUE, fig=gridFIG())
plot(x = 1:10, y = 10:1)
# done with the first viewport
popViewport()
# move to the next viewport
pushViewport(vp.2)
ggplotted <- qplot(x=1:10,y=10:1, 'point')
# print our ggplot graphics here
print(ggplotted, newpage = FALSE)
# done with this viewport
popViewport(1)
This example is a modified version of this blog post by Dylan Beaudette
Yes. They are both grid-based graphics systems and return graphical objects. Take a look at the grid.arrange function in gridExtra package
I’d really appreciate your help with the following problem. I know several ways to save a single plot to a file. My question is: How do I correctly save a multiplot to a file?
To begin with, I’m not an experienced R user. I use ggplot2 to create my plots, and another thing I should probably mention is that I use the RStudio GUI. Using an example from the R Cookbook, I'm able to create multiple plots in one window.
I would like to save this so-called multiplot to a file (preferably as jpeg), but somehow fail to do this.
I’m creating the multiplot as follows:
##define multiplot function
multiplot <- function(..., plotlist=NULL, cols) {
require(grid)
# Make a list from the ... arguments and plotlist
plots <- c(list(...), plotlist)
numPlots = length(plots)
# Make the panel
plotCols = cols # Number of columns of plots
plotRows = ceiling(numPlots/plotCols) # Number of rows needed, calculated from # of cols
# Set up the page
grid.newpage()
pushViewport(viewport(layout = grid.layout(plotRows, plotCols)))
vplayout <- function(x, y)
viewport(layout.pos.row = x, layout.pos.col = y)
# Make each plot, in the correct location
for (i in 1:numPlots) {
curRow = ceiling(i/plotCols)
curCol = (i-1) %% plotCols + 1
print(plots[[i]], vp = vplayout(curRow, curCol ))
}
}
## define subplots (short example here, I specified some more aesthetics in my script)
plot1a <- qplot(variable1,variable2,data=Mydataframe1)
plot1b <- qplot(variable1,variable3,data=Mydataframe1)
plot1c <- qplot(variable1,variable2,data=Mydataframe2)
plot1d <- qplot(variable1,variable3,data=Mydataframe2)
## plot in one frame
Myplot <- multiplot(plot1a,plot1b,plot1c,plot1d, cols=2)
This gives the desired result. The problem arises when I try to save to a file. I can do this manually in RStudio (using Export -> Save plot as image), but I would like to run everything in a script. I manage to save only subplot1d (which is last_plot()), and not the complete multiplot.
What I’ve tried so far:
Using ggsave
ggsave(filename = "D:/R/plots/Myplots.jpg")
This results in only subplot 1d being saved.
Using jpeg(), print() and dev.off()
jpeg(filename = "Myplot.jpg", pointsize =12, quality = 200, bg = "white", res = NA, restoreConsole = TRUE)
print(Myplot)
dev.off()
This results in a completely white image (just the background I assume). print(Myplot) returns NULL.
Not sure what I’m doing wrong here. My lack of understanding R is the reason I am stuck trying to find a solution. Can anyone explain what I’m doing wrong and perhaps suggest a way to solve my problem(s)?
Its because Myplot is the returned value from your multiplot function, and it returns nothing (its job is to print the graphs). You need to call multiplot with the jpeg device open:
jpeg(filename = "Myplot.jpg", pointsize =12, quality = 200, bg = "white", res = NA, restoreConsole = TRUE)
multiplot(plot1a,plot1b,plot1c,plot1d, cols=2)
dev.off()
should work.
Using the example code (R cookbook), it works for me
png("chickweight.png")
multiplot(p1, p2, p3, p4, cols=2)
dev.off()
And for completeness sake, ggsave does not work as it only saves the last printed ggplot object, which in your case is just the last plot. This is caused by the fact that multiplot creates the plot by drawing the ggplot objects onto different subsets of the total graphics device. An alternative is to create the plot by combining the ggplot objects into one big ggplot object, and then printing the object. This would be compatible with ggsave. This approach is implemented by arrangeGrob in the gridExtra package.