There is very convenient way of plotting multiple graphs and that's with gridExtra - grid.arrange:
grid.arrange(plot1,plot2,plot3,plot4,plot5,plot6,plot7,plot8,plot9, ncol=3)
The above command draws 3x3 graphs in one window.
Now, I'm using my own lattice setup to draw unique lines etc. via
trellis.par.set(my.setup)
However using the grid.arrange command for plotting multiple plots won't pass on the setup as the output plots are in default colours.
So the question is how to pass on the my.setup onto grid.arrange or alternatively how to plot easily multiple graphs in one go for lattice.
EDIT: Reproducible example:
Data <- data.frame(Col1=rnorm(10,0,1),Col2=rexp(10,2),Col3=rnorm(10,2,2),Col4=runif(10,0,2),
Time=seq(1,10,1))
trellis.par.set(col.whitebg())
newSet <- col.whitebg()
newSet$superpose.symbol$col <- c("blue3","orange2","gray1","tomato3")
newSet$superpose.symbol$pch <- 1
newSet$superpose.symbol$cex <- 1
newSet$superpose.line$col <- c("blue3","orange2","gray1","tomato3")
trellis.par.set(newSet)
Plot1 <- xyplot(Col1+Col2~Time, Data, type="spline")
Plot2 <- xyplot(Col2+Col3~Time, Data, type="spline")
Plot3 <- xyplot(Col1+Col3~Time, Data, type="spline")
Plot4 <- xyplot(Col3+Col4~Time, Data, type="spline")
grid.arrange(Plot1,Plot2,Plot3,Plot4, ncol=2)
I guess it's got something to do with the plot.trellis method not finding the global theme settings when it's wrapped in gridExtra::drawDetails.lattice. I don't understand these lattice options, but as far as I recall you can specify them explicitly at the plot level too,
pl = list(Plot1, Plot2, Plot3, Plot4)
# do.call(grid.arrange, c(pl, nrow=1))
do.call(grid.arrange, c(lapply(pl, update, par.settings=newSet), list(nrow=1)))
Related
I would like to generate multiple plots using marginplot() (VIM package) and then arrange them into one big figure. I tried to use grid.arrange (grid/gridExtra package) and it did not work. The error was, that a grob was expected as input. So I tried to first convert the marginplot into a ggplot (as.ggplot) or grob (as.grob) but this did not work. Has anyone an idea how to arrange the plots?
library(VIM)
library(ggplotify)
library(grid)
library(gridExtra)
x <- cars[, c("speed", "dist")]
marginplot(x)
y <- cars[, c("speed", "dist")]
marginplot(y)
p <- qplot(1,1)
#p2 <- as.ggplot(marginplot(x))
r <- rectGrob(gp=gpar(fill="grey90"))
grid.arrange( r, p,p, r, ncol=2)
I created a small code with cars, where I managed to arrange grey squares and qplots. put I cannot add the marginplot.
With base plots this error occurs. Learned here: grid.arrange from gridExtras exiting with "only 'grobs' allowed in 'gList'" after update
grid.arrange is intended to be used with "grid graphical objects" (grobs), such as ggplot2.
One could find an equivalent grid-plot or use a base-graphics approach to stacking plots.
Try this:
library(VIM)
x <- cars[, c("speed", "dist")]
y <- cars[, c("speed", "dist")]
par(mfrow = c(2,2))
marginplot(x)
marginplot(y)
plot(rnorm(100))
hist(rnorm(100))
par(mfrow = c(1, 1)) #reset this parameter
I'd like to make an object that has a QQ chart
This is my code
qqnorm(titanic$age)
qqline(titanic$age)
In ggplot, I can layer geoms on top of each other, so they can be in one object
What's the equivalent for this case?
Here's some code as an example. I had to use a different dataset, as the "Titanic" dataset's age column is non-numeric:
data("AirPassengers")
qqnorm(AirPassengers)
qqline(AirPassengers)
lines(x = 1:length(AirPassengers), rep(300, 144))
p <- recordPlot()
p
edit: to disable the plot:
dev.control('inhibit')
plot(rnorm(10))
p <- recordPlot()
dev.off()
in a loop:
for(i in 1:10){
# dev.control('inhibit')
plot(rnorm(10))
p <- recordPlot()
# dev.off()
l_plots[[i]] <- p
}
Somehow it seems difficult to combine the approaches. How about you just delete the plots in the plotting window after creating them?
I'm attempting to plate two plots in the same .jpg using arrangeGrob().
I've only just started learning about grids and grobs and I think I know what the problem is: pheatmap is a grid object and containing grob objects, not allowing me to put it in arrangeGrob. Is this true?
Would I somehow need to put the qplot in a grid and the pheatmap in a grid and then put those grids in a new grid?
library(grid)
library(gridExtra)
library(pheatmap)
library(ggplot2)
hmdat=rbind(c(1,2,3),
c(3,4,5),
c(5,6,7))
hm=pheatmap(hmdat)
qp=qplot(1,1)
lm=rbind(c(1,2,2),
c(1,2,2))
jpeg("plots.jpg")
arrangeGrob(qp,hm, layout_matrix=lm)
dev.off()
The above code snippet runs just fine when using
arrangeGrob(qp,qp, layout_matrix=lm)
I'm not sure if you wanted to have 6 figures or you wanted to have two figures one with twice as wide as the other one (I tried to do minimum code change):
library("grid")
library("gridExtra")
library("pheatmap")
library("ggplot2")
hmdat=rbind(c(1,2,3),
c(3,4,5),
c(5,6,7))
hm <- pheatmap::pheatmap(hmdat)
qp <- qplot(1,1)
lm <- rbind(c(1,2,2),
c(1,2,2))
grid.arrange(grobs = list(qp,hm[[4]]), layout_matrix = lm)
which will give you:
The same way you can have multiple pheatmaps side-by-side:
library("grid")
library("gridExtra")
library("pheatmap")
hmdat <- rbind(c(1,2,3),
c(3,4,5),
c(5,6,7))
hm <- pheatmap::pheatmap(hmdat)
lm <- rbind(c(1,2),
c(3,3))
grid.arrange(grobs = list(hm[[4]],
hm[[4]],
hm[[4]]),
layout_matrix = lm)
As #hrbrmstr mentioned in the comment, you should use the 4th item in the pheatmap object. Also remember to provide grobs as list to the grid.arrange
I have a working loop which generates and can save individual plots from each file saved in a directory.
I want to plot all of the returned plots in a single file as a 2x2 grid over multiple pages but cannot do this.
I have tried to save the plot objects in a list
pltList <- list()
pltList[]
for (f in 1:length(files)){
plot_object <- ggplot2(...) #make ggplot2 plot
print(plot_object)
pltList[[f]] <- plot_object #save ggplot2 plot in list
}
jpeg(filename.jpg)
par(mfrow=c(2,2)) #to generate 2x2 plot per page
print(pltList[[1]])
print(pltList[[2]])
...
print(pltList[[f]])
dev.off()
The problem is that the resulting saved .jpg file only contains the last plot and not a 2x2 grid of all plots over many pages which is what I want.
EDIT
My first problem is how to save each plot from the loop in the list - how can I view the saved objects from the list to make sure they have been saved correctly?
When I do print(pltList[1]), the resulting output is:
function (x, y, ...)
UseMethod("plot")
<bytecode: 0x0000000010f43b78>
<environment: namespace:graphics>
rather than the actual plot. It seems that the plots are not being saved in the list as expected. How can I correct for this?
Hopefully, once this is fixed, your plotting suggestions will work.
I did recently the same. I used grid.arrange().
library(ggplot2)
library(gridExtra)
library(grid)
p1<-ggplot()+geom_line(aes(x=1:10,y=1:10))
p2<-ggplot()+geom_line(aes(x=1:10,y=1:10))
p3<-ggplot()+geom_line(aes(x=1:10,y=1:10))
p4<-ggplot()+geom_line(aes(x=1:10,y=1:10))
grid.arrange(p1,p2,p3,p4, ncol=1, top=textGrob("Multiple Plots", gp=gpar(fontsize=12, font = 2)))
Assuming you need a PDF output where every page has multiple plots plotted as one, e.g.: if there are 12 plots then 4 plots per page.
Try this example:
library(ggplot2)
library(cowplot)
# list of 12 dummy plots, only title is changing.
pltList <- lapply(1:12, function(i){
ggplot(mtcars,aes(mpg,cyl)) +
geom_point() +
ggtitle(paste("Title",i))})
# outputs 3 jpeg files with 4 plots each.
for(i in seq(1,12,4))
ggsave(paste0("Temp",i,".jpeg"),
plot_grid(pltList[[i]],
pltList[[i+1]],
pltList[[i+2]],
pltList[[i+3]],nrow = 2))
# or we can output into 1 PDF with 3 pages using print
pdf("TempPDF.pdf")
for(i in seq(1,12,4))
print(plot_grid(pltList[[i]],
pltList[[i+1]],
pltList[[i+2]],
pltList[[i+3]],nrow = 2))
dev.off()
EDIT:
Another way using gridExtra, as suggested by #user20650:
library(gridExtra)
#output as PDF
pdf("multipage.pdf")
#use gridExtra to put plots together
marrangeGrob(pltList, nrow=2, ncol=2)
dev.off()
I'd like to combine multiple effect plots in one window with the effects package, but don't know if there is an easy way to do so.
Here's an example that doesn't work:
d1 <-data.frame(x1=rnorm(100,0:10),y1=rnorm(100,0:10),x2=rnorm(100,0:10),y2=rnorm(100,0:10))
require(effects)
require(gridExtra)
plot1 <- plot(allEffects(mod=lm(y1~x1,d1)))
plot2 <- plot(allEffects(mod=lm(y2~x2,d1)))
grid.arrange(plot1,plot2,ncol=2)
I think you need to collect the values of allEffects components and then plot them as an 'efflist'. It looked to me that the plotting was base-graphics, but it is in fact 'lattice' if you follow the class-function trail (or if you read: ?plot.efflist )
Try this:
ef1 <-allEffects(mod=lm(y1~x1,d1))[[1]]
ef2 <- allEffects(mod=lm(y2~x2,d1))[[1]]
elist <- list( ef1, ef2 )
class(elist) <- "efflist"
plot(elist, col=2)
Interestingly, the result from plotting an efflist (which is the result from allEffects) is not a lattice graphic; it instead builds up a multipanel graphic of lattice graphics using the print.lattice methods. However, if you plot the individual effects, either by taking the elements from allEffects or by using effect, then you do get lattice graphics.
Either like this
p1 <- plot(allEffects(m1)[[1]])
p2 <- plot(allEffects(m2)[[1]])
or like this.
p1 <- plot(effect("x1", m1))
p2 <- plot(effect("x2", m2))
These can be combined with grid.arrange; the catch is that their class is c("plot.eff", "trellis") which grid.arrange doesn't recognize, so they have to be made into simple trellis objects first.
class(p1) <- class(p2) <- "trellis"
grid.arrange(p1, p2, ncol=2)