As indicated in the title above, I want to change the column labels in the heatmap figure produced by heatmap.2 from package gplots in R to symbols rather than text. May I know if it is possible, and if so, how to do it?
This is a sample code to generate heatmap using heatmap.2:
library(gplots)
data<-sample(1:100,size=80)
M<-matrix(data,nrow=10,ncol=8)
colnames(M)<-c("W1_1","W1_2","W1_3","W1_4","B1_1","B1_2","B1_3","B1_4")
heatmap.2(M, trace="none", dendrogram="none")
This is the heatmap result:
In this case, the column labels are "W1_1","W1_2","W1_3","W1_4","B1_1","B1_2","B1_3","B1_4". May I know If it is possible to use two symbols to represent W1 and B1 group respectively and show in the final figure.
I have attached a sample below (changed via photoshop):
Thanks in advance for all the helps!
Here's another possibility with standard image function:
op <- par(mar=c(4,2,2,4))
image(seq(nrow(M)), seq(ncol(M)), M, axes=F, xlab="", ylab="")
axis(side=4, at=seq(ncol(M)))
par(xpd=TRUE)
points(seq(nrow(M)), rep(0, nrow(M)),
pch=c(16, 15), col=c("cyan", "pink"), cex=2
)
par(op)
Related
Purpose
Create scatter plot with third dimension and multiple colors.
First:
- 3rd dimension with another scale in contrast to y-axis
- create two colors (this is done using col, see code)
Sketch simulating the purpose:
Code
Two "containers" of points plotted in this way:
plot(1:3, c(3,3,3))
points(1:3, c(2,2,2), col="blue")
Another nice plotting is done by:
#install.packages("hexbin")
library(hexbin)
x <- 1:1000#rnorm(1000)
y <- 1500:501#rnorm(1000)
bin<-hexbin(x, y, xbins=50)
plot(bin, main="Hexagonal Binning")
But I do not know how to use hexbin (I do not understand the functionality). There are needed two colors which I do not know how to generate.
Questions
How to create the 3rd axis with other scaling than the y-axis?
Can I use ´hexbin´ to get the result?
For some reason, using points() does not work, but using plot() does work:
#Set margin on right side to be a bit larger
par(mar = c(5,4.5,4,5))
#Plot first set of data
plot(1:3, rep(3,3), ylim=c(-5,5), xlab="X-Axis", ylab="Y-Axis 1")
#Plot second set of data on different axis.
par(new=T)
plot(1:3, rep(5,3), ylim=c(-10,10), col="blue", xlab="", ylab="", axes=FALSE)
#Add numbers and labels to the second y-axis
mtext("Y-Axis 2",side=4,line=3)
axis(4, ylim=c(-10,10))
I have plotted a histogram in R and marked quantiles using abline() in vertical intervals. However, I want to plot a legend that shows the corresponding values to the quantiles together with the quantile interval itself.
The current legend is almost there as you can see if you run the example code below. But I can't seem to succeed at aligning the legend interval with its corresponding value and colored line symbol. I tried to use a data.frame() to achieve this but it didn't work out.
Any tips or suggestions will be very much appreciated.
x<-1:100
quantiles_x<-quantile(x)
hist(x)
abline(v=quantiles_x, col=c("blue", "green","red","yellow","black"))
legend('topright', legend=c(names(quantiles_x), levels(factor(quantiles_x))), lwd=1, col=c("blue","green","red","yellow","black"))
Something like this??
x<-1:100
quantiles_x<-quantile(x)
hist(x)
abline(v=quantiles_x, col=c("blue", "green","red","yellow","black"))
labels <- paste(names(quantiles_x), "[",quantiles_x,"]")
legend('topright', legend=labels, lwd=1,
col=c("blue","green","red","yellow","black"))
I want to plot a centered legend outside of the plotting area in a device having multiple plots. There has been many questions (with slight variations) asked in SO about changing the position of legend in a R plot.
For example:
1) R - Common title and legend for combined plots
2) Common legend for multiple plots in R
3) Plot a legend outside of the plotting area in base graphics?
etc.
Now what I understood from the above questions is that I got to set the option xpd = T or xpd = NAto plot legends at the outer margins. However when I try this, it somehow does not work for me ..
par(mfrow=c(1,2),oma=c(0,3,0,0),xpd=TRUE)
plot(c(5,10),col=c("red","blue"),pch=20,cex=2,bty="n",xlab="",ylab="")
barplot(c(5,10),col=c("red","blue"))
mtext(text="My two plots",side=3,cex=2,outer=TRUE,line=-3)
legend("top",legend=c("A", "B"),fill=c("red","blue"),ncol=2,xpd=NA,bty="n") # Option 1
legend(x=0.01,y=11,legend=c("A", "B"),fill=c("red","blue"),ncol=2,xpd=TRUE,bty="n") # Option 2
Now my question is, how does xpd exactly work ? as I am unable to figure out why shouldn't the legend not be placed outside the plot area with xpd=T.
I apologize in advance if some consider this as a duplicate of the above questions !!
Help is much appreciated
Ashwin
Option #1 is likely the route you should take, with xpd=NA. It does not automatically place the legend in the outer margins, but it allows you to place the legend anywhere you want. So, for example, you could use this code to place the legend at the top of the page, approximately centered.
legend(x=-1.6, y=11.6, legend=c("A", "B"), fill=c("red", "blue"), ncol=2, xpd=NA, bty="n")
I chose these x and y values by trial and error. But, you could define a function that overlays a single (invisible) plot on top of the ones you created. Then you can use legend("top", ...). For example
reset <- function() {
par(mfrow=c(1, 1), oma=rep(0, 4), mar=rep(0, 4), new=TRUE)
plot(0:1, 0:1, type="n", xlab="", ylab="", axes=FALSE)
}
reset()
legend("top", legend=c("A", "B"), fill=c("red", "blue"), ncol=2, bty="n")
I also had a hard time to get coordinates on the margins. I think I found a solution, you can specify coordinates for the legend using:
getCoords() function.
Look also to legend_margin function from plotfunctions package.
So combining the solution from Jean V. Adams with one of these functions should get you there.
Hope that works :)
Struggling with this one. I have 25 data items that I want plotted with bubbles in 5 columns.
The plot can be re-created thus:
xcord <- c(1,1,1,1,1,2,2,2,2,2,3,3,3,3,3,4,4,4,4,4,5,5,5,5,5)
ycord <- c(1,2,3,4,5,1,2,3,4,5,1,2,3,4,5,1,2,3,4,5,1,2,3,4,5)
zsize <- c(2,1,2,3,6,8,9,1,4,5,5,6,7,8,8,9,5,5,5,5,1,8,1,1,12)
Save the parameters before I change them:
op <- par()
dev.off()
Change the parameters:
par (mfrow=c(1,0), mar=c(2,2,2,2), oma=c(2,2,2,2))
Plot using symbols:
symbols(xcord, ycord, zsize, inches=0.3, fg="white", bg="red", xlab="Events", ylab="Diagnoses", tck=0, xaxt="n", yaxt="n")
mtext("Rheumatic diagnoses by cerebrovasular events", line=2, font=2, cex=1.2)
I am happy with the above plot and deliberately used tck=0, xaxt="n", yaxt="n" to clear the axes. I want to manually overlay custom text, controlled with custom co-ordinates (which work with the sysmbols plot), but have not been able to do it. I have tried some of the par arguments and the axes function.
I also tried leaving the axes on:
symbols(xcord, ycord, zsize, inches=0.3, fg="white", bg="red", xlab="Events", ylab="Diagnoses")
but do not know how to change the output (1,2,3,4,5) to my own custom axes labels.
Thank you.
You are looking for the axis function (see ?axis for details), e.g. to replace the 1:5 with A, B, C, D, E:
axis(side=1, at=1:5, labels=LETTERS[1:5])
I used the information from this post to create a histogram with logarithmic scale:
Histogram with Logarithmic Scale
However, the output from plot looks nothing like the output from hist. Does anyone know how to configure the output from plot to resemble the output from hist? Thanks for the help.
A simplified, reproducible version of the linked answer is
x <- rlnorm(1000)
hx <- hist(x, plot=FALSE)
plot(hx$counts, type="h", log="y", lwd=10, lend="square")
To get the axes looking more "hist-like", replace the last line with
plot(hx$counts, type="h", log="y", lwd=10, lend="square", axes = FALSE)
Axis(side=1)
Axis(side=2)
Getting the bars to join up is going to be a nightmare using this method. I suggest using trial and error with values of lwd (in this example, 34 is somewhere close to looking right), or learning to use lattice or ggplot.
EDIT:
You can't set a border colour, because the bars aren't really rectangles – they are just fat lines. We can fake the border effect by drawing slightly thinner lines over the top. The updated code is
par(lend="square")
bordercol <- "blue"
fillcol <- "pink"
linewidth <- 24
plot(hx$counts, type="h", log="y", lwd=linewidth, col=bordercol, axes = FALSE)
lines(hx$counts, type="h", lwd=linewidth-2, col=fillcol)
Axis(side=1)
Axis(side=2)
How about using ggplot2?
x <- rnorm(1000)
qplot(x) + scale_y_log10()
But I agree with Hadley's comment on the other post that having a histogram with a log scale seems weird to me =).