Plot a table with box size changing

Question

Does anyone have an idea how is this kind of chart plotted? It seems like heat map. However, instead of using color, size of each cell is used to indicate the magnitude. I want to plot a figure like this but I don't know how to realize it. Can this be done in R or Matlab?

Arvy

Answer 1

Try scatter:

scatter(x,y,sz,c,'s','filled');

where x and y are the positions of each square, sz is the size (must be a vector of the same length as x and y), and c is a 3xlength(x) matrix with the color value for each entry. The labels for the plot can be input with set(gcf,properties) or xticklabels:

X=30;
Y=10;
[x,y]=meshgrid(1:X,1:Y);
x=reshape(x,[size(x,1)*size(x,2) 1]);
y=reshape(y,[size(y,1)*size(y,2) 1]);

sz=50;
sz=sz*(1+rand(size(x)));
c=[1*ones(length(x),1) repmat(rand(size(x)),[1 2])];
scatter(x,y,sz,c,'s','filled');

xlab={'ACC';'BLCA';etc}
xticks(1:X)
xticklabels(xlab)
set(get(gca,'XLabel'),'Rotation',90);
ylab={'RAPGEB6';etc}
yticks(1:Y)
yticklabels(ylab)

EDIT: yticks & co are only available for >R2016b, if you don't have a newer version you should use set instead:

set(gca,'XTick',1:X,'XTickLabel',xlab,'XTickLabelRotation',90) %rotation only available for >R2014b
set(gca,'YTick',1:Y,'YTickLabel',ylab)

Formalize

Can you please provide information about the packages you are using – Jaunita

@Jaunita - this is Matlab, no packages, just toolboxes, and in this case none of them is needed. – Dwanadwane

Nice. You should replace xticks, xticklabels, yticks, yticklabels with set or HG2 commands (i.e. ax = gca, ax.XTick and so on...), as this code results in an error. – Dwanadwane

Answer 2

In R, corrplotpackage can be used. Specifically, you have to use method = 'square' when creating the plot.

Try this as an example:

library(corrplot)
corrplot(cor(mtcars), method = 'square', col = 'red')

Jaunita

Answer 3

in R, you should use ggplot2 that allows you to map your values (gene expression in your case?) onto the size variable. Here, I did a simulation that resembles your data structure:

my_data <- matrix(rnorm(8*26,mean=0,sd=1), nrow=8, ncol=26,
                  dimnames = list(paste0("gene",1:8), LETTERS))

Then, you can process the data frame to be ready for ggplot2 data visualization:

library(reshape)
dat_m <- melt(my_data, varnames = c("gene", "cancer"))

Now, use ggplot2::geom_tile() to map the values onto the size variable. You may update additional features of the plot.

library(ggplot2)
ggplot(data=dat_m, aes(cancer, gene)) + 
  geom_tile(aes(size=value, fill="red"), color="white") + 
  scale_fill_discrete(guide=FALSE) + ##hide scale
  scale_size_continuous(guide=FALSE) ##hide another scale

Burrstone

Side note: If you happen to use the Tableau software (which may require a subscription or license), it appears that there are features that allow you to make the plot you want: onlinehelp.tableau.com/current/pro/desktop/en-us/… – Burrstone