I would like two plots to show up in two seperate spaces in the plot so I do:
par(mfrow=c(1,2))
plot(1:10,1:10)
Now I would like the second plot to be about 25% shorter than the first plot so I adjust omd:
tmp <- par()$omd
tmp[4] <- 0.75
par(omd=tmp)
plot(1:10,1:10)
The problem is that the second plot shows up ontop of the first plot. How do I avoid this margin issue?
Maybe try using layout instead?
layout(matrix(c(1, 1, 0, 2), ncol = 2L), widths = c(1,1),heights = c(0.5,1))
par(mar = c(3,2,2,2))
plot(1:10,1:10)
par(mar = c(3,2,2,2))
plot(1:10,1:10)
I guess maybe you'd want to set the heights to c(0.2,0.8) to get a 25% reduction?
Edit
But I don't think that omd does what you think it does. It changes the region inside the outer margins, which will always include both plot regions when setting par(mfrow = c(1,2)). What you really want to change, I think is plt, which alters the size of the current plotting region (using quartz, as I'm on a mac):
quartz(width = 5,height = 5)
par(mfrow=c(1,2))
vec <- par("plt")
plot(1:10,1:10)
par(plt = vec * c(1,1,1,0.75))
plot(1:5,1:5)
Related
I made a matrix of figures using par(mfrow = (3, 4)). Now I want to overlay each row with texts like this:
What is the simplest way to achieve this?
Thank you!
OPTION 1
Add the text after plotting all figures:
par(list(mfrow = c(3, 4),
mar=c(2,2,1,1)))
lapply(1:12,FUN=function(x) plot(1:100,runif(100),cex=0.2))
##You will have to manually adjust these values to fit your figure
xval = -150
yval = 0.5
y_incr = 1.59
text(x=xval, y=yval, labels="TextToAdd3",col=rgb(0,0,1,0.5), cex=3, xpd=NA)
text(x=xval, y=yval+y_incr, labels="TextToAdd2",col=rgb(0,0,1,0.5), cex=3, xpd=NA)
text(x=xval, y=yval+y_incr*2, labels="TextToAdd1",col=rgb(0,0,1,0.5), cex=3, xpd=NA)
OPTION 2
Centre caption on the left margin every time you plot in the third column. This means less stuffing around with manually adjusting values (plot looks the same as above):
par(list(mfrow = c(3, 4),
mar=c(2,2,1,1)))
texts=list("TextToAdd1",
"TextToAdd3",
"TextToAdd3")
for(i in 1:12){
plot(1:100,runif(100),cex=0.2)
if((i+1)%%4==0){
mtext(text=texts[[i/3]],side=2,line=par()$mar[2], las=1,col=rgb(0,0,1,0.5), cex=3,adj=0.5)
}
}
I'm wondering - is there any way how to add labels of clusters into dendrogram. See simple example:
hc = hclust(dist(mtcars))
plot(hc, hang = -1)
rect.hclust(hc, k = 3, border = "red")
Desired output should look like this:
Thanks for any suggestions!
You need to get the coordinates of the place to put your clusters' labels:
First axis:
As you are calling rect.hclust, you might as well assign the result so you can use it to find the beginning of clusters (the first one begins at 1 the 2nd at 1 + the length of the first, etc.
rh <- rect.hclust(hc, k = 3, border = "red")
beg_clus <- head(cumsum(c(1, lengths(rh))), -1)
Second axis:
You just want to be above the red rectangle, which is at the middle of the height where you have k-1 clusters and the height where you have k clusters. Let's say you're aiming at 4/5 of the distance instead of 1/2:
y_clus <- weighted.mean(rev(hc$height)[2:3], c(4, 1))
Putting the labels:
text(x=beg_clus, y=y_clus, col="red", labels=LETTERS[1:3], font=2)
An alternative to adding text labels is in the mjcgraphics package that deals with cluster labels. See https://github.com/drmjc/mjcgraphics and https://rdrr.io/github/drmjc/mjcgraphics/man/rect.hclust.labels.html
rect.hclust.labels(hc, k=3, border = 1 ) # adds labels to clusters
I am using library VennDiagram to plot venn diagrams. But this function does not have a functionality to add legend and set names are displayed on or close to the sets themselves.
library(VennDiagram)
x <- list(c(1,2,3,4,5),c(4,5,6,7,8,9,10))
venn.diagram(x,filename="test.png",fill=c("#80b1d3","#b3de69"),
category.names=c("A","B"),height=500,width=500,res=150)
And with many sets, overplotting names is an issue and I would like to have a legend instead. The function is built on grid graphics and I have no idea how grid plotting works. But, I am attempting to add a legend anyway.
Looking into the venn.diagram function, I find that final plotted object is grob.list and it is a gList object and its plotted using grid.draw().
png(filename = filename, height = height, width = width,
units = units, res = resolution)
grid.draw(grob.list)
dev.off()
I figured out that I could create a legend by modifying the venn.diagram function with the code below.
cols <- c("#80b1d3","#b3de69")
lg <- legendGrob(labels=category.names, pch=rep(19,length(category.names)),
gp=gpar(col=cols, fill="gray"),byrow=TRUE)
Draw the object lg
png(filename = filename, height = height, width = width,
units = units, res = resolution)
grid.draw(lg)
dev.off()
to get a legend
How do I put the venn diagram (gList) and the legend (gTree,grob) together in a usable way? I am hoping to get something like base plot style:
or the ggplot style
If you are allowed to use other packages than VennDiagram, I suggest the following code using the eulerr package:
library(eulerr)
vd <- euler(c(A = 5, B = 3, "A&B" = 2))
plot(vd, counts = TRUE,lwd = 2,
fill=c("#80b1d3","#b3de69"),
opacity = .7,
key = list( space= "right", columns=1))
with key you define the legend location and appearance.
If you want to continue using the VennDiagram package and learn a bit of grid on the way:
Prepare diagram and legend
library(VennDiagram)
x <- list(c(1,2,3,4,5),c(4,5,6,7,8,9,10))
diag <- venn.diagram(x,NULL,fill=c("#80b1d3","#b3de69"),
category.names=c("A","B"),height=500,width=500,res=150)
cols <- c("#80b1d3","#b3de69")
lg <- legendGrob(labels=c("A","B"), pch=rep(19,length(c("A","B"))),
gp=gpar(col=cols, fill="gray"),
byrow=TRUE)
Transform the diagram to a gTree
(I'd love to find a better way if anyone knows one)
library(gridExtra)
g <- gTree(children = gList(diag))
Plot the two gTrees side by side
gridExtra::grid.arrange(g, lg, ncol = 2, widths = c(4,1))
Or one above the other
grid.arrange(g, lg, nrow = 2, heights = c(4,1))
I have found a solution as well, but the venn diagram region is not square aspect ratio. And the legend is not spaced ideally.
library(gridGraphics)
png("test.png",height=600,width=600)
grab_grob <- function(){grid.echo();grid.grab()}
grid.draw(diag)
g <- grab_grob()
grid.arrange(g,lg,ncol=2,widths=grid::unit(c(0.7,0.3),"npc"))
dev.off()
I am trying to plot a Rgraphviz object with two edge labels. Unfortunately the labels fall outside the plot. Here is my example:
require('Rgraphviz')
set.seed(123)
g1 <- randomGraph(letters[1:10], 1:4, 0.4)
eAttrs <- list()
eAttrs$label <- c("a~g" = "I have a very long label 1", "a~i" = "and a long label 2")
plot(g1, edgeAttrs = eAttrs)
Here is my plot:
I tried several things with no success:
1.
Set a larger bounding box
z <- agopen(g1, "foo")
z#boundBox#upRight#x <- z#boundBox#upRight#x + 300
z#boundBox#upRight#y <- z#boundBox#upRight#y + 300
plot(z, edgeAttrs = eAttrs)
2.
Decrease the label fontsize (not really what I want in my application, anyways)
eAttrs$labelfontsize=c("a~g"="3")
plot(g1, edgeAttrs = eAttrs)
3.
Change par attributes:
par(oma=c(10,10,10,10))
plot(g1, edgeAttrs = eAttrs)
4.
Change node, edge and general attributes from ?Rgraphviz::GraphvizAttributes
attrs <- list(graph=list(size=c(1, 1)))
attrs$edge$fontsize<-8
plot(g1, edgeAttrs = eAttrs, attrs=attrs)
None of my attempts seem to work. Does anyone have an idea?
The problem
Calling plot() on a graph object dispatches an S4 method (shown by getMethod("plot", "graph")), which in turn calls the function shown by typing getMethod("plot", "Ragraph"). That function contains the following rather unfortunate lines which, regardless of any related parameter settings you've made, will override them to reset the left and right margins to 0. Frustrating!
oldpars <- par(mai = c(sheight, 0, mheight, 0))
on.exit(par(oldpars), add = TRUE)
A workaround
One workaround is to construct a three panel layout in which the left and right panels are just there to provide a bit of buffering space. Turn off clipping, plot your graph object in the middle panel, and it then seems to work:
layout(matrix(1:3, nrow=1), widths=c(1,5,1))
par(xpd=NA) ## turn off all clipping
plot.new() ## blank plot in Panel 1
plot(g1, edgeAttrs = eAttrs) ## graph in Panel 2
plot.new() ## blank plot in Panel 3
I found another solution: In my original question I changed the size of the bounding box in a laid out graph I got with agopen. Plotting the laid out graph showed no edge labels at all. I found that it is possible to pass the edge attributes from the graph object to agopen and then change the bounding box:
require('Rgraphviz')
set.seed(123)
g1 <- randomGraph(letters[1:10], 1:4, 0.4)
eAttrs <- list()
eAttrs$label <- c("a~g" = "I have a very long label 1", "a~i" = "and a long label 2")
z <- agopen(g1, "foo", edgeAttr=eAttrs)
z#boundBox#botLeft#x <- z#boundBox#botLeft#x - 400 ##left
z#boundBox#upRight#x <- z#boundBox#upRight#x + 200 ##right
plot(z)
The plot:
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')