Hi, everyone
Do you known how thay get this type of pictures? Thank you!
I known seqMiner can give this type of picture, but I have to work on server(only command line available) for it will cost lots of memory. Can this be finished by R or other programming languages?
The input data format may like this, several groups of data, each group has same columns:
# grp1 grp2 grp3
Gene 1 2 3 4 1 2 3 4 1 2 3 4
a 0.1 0.2 0.3 0.4 0.1 0.2 0.3 0.4 0.1 0.2 0.2 0.4
b 0.1 0.2 0.3 0.4 0.1 0.2 0.3 0.4 0.1 0.2 0.2 0.4
c 0.1 0.2 0.3 0.4 0.1 0.2 0.3 0.4 0.1 0.2 0.2 0.4
d 0.1 0.2 0.3 0.4 0.1 0.2 0.3 0.4 0.1 0.2 0.2 0.4
e 0.1 0.2 0.3 0.4 0.1 0.2 0.3 0.4 0.1 0.2 0.2 0.4
f 0.1 0.2 0.3 0.4 0.1 0.2 0.3 0.4 0.1 0.2 0.2 0.4
And also when using heatmap.2 to draw heatmap for lots of data, it will take a large amount of time. Is there any fast tools to solve it?
Thank you!
•
written
by
chentong.biology •
This should get you started. You'll require packages ggplot2 and reshape2. I don't see any clustering here. Hope I'm right.
require(ggplot2)
require(reshape2)
x <- as.data.frame( matrix(rnorm(1200,100,35), ncol=12) )
names(x) <- paste( "g", sort(rep(1:3,4)), rep(1:4,3), sep="")
head(x)
x$id <- paste( "gene", 1:dim(x)[1], sep="")
x.m <- melt( x, c("id"), names(x)[1:12] )
x.m$grp <- c( rep("g1",400), rep("g2",400), rep("g3",400) )
x.m$grp <- factor(x.m$grp, levels=c("g1","g2","g3"), ordered=T )
x.m <- subset( x.m, select=c(grp, id, variable, value) )
p <- ggplot( data=x.m, aes(variable, id)) + geom_tile(aes(fill = value), colour = "white") + scale_fill_gradient(low = "white", high = "steelblue")
p <- p + facet_grid( .~grp, scale="free")
p
This is how it looks. You can build on this as you want. In case you don't follow, let me know. I'll try to comment the code later.
Good work, but R cries when the list (before melting) > 10K-15K and with facets, launch the code and go out for a walk. Then, best is to remove the labels on y axis. Also, concerning clustering one never knows, it might be centroid :)
Are you running it on parallel nodes, which lib are you using for that or a custom code
Yeah yeah, I got it, one can also use 'ff' for loading.
Cheers
Do you mean "p + opts(axis.ticks=themeblank(), axis.text=themeblank()) "?
yeah, just the axis.text should be axis.text.y, because x axis is fine, just y axis is cluttered up
Great great answer, Thanks Arun! I wonder if I can cluster data first, then do the heatmap?
Thanks, I solved it by using kmeans.
Obtain coverage for your factor within certain range like +/-2.5 kb with a binsize like 50 and then load this matrix in javatree view. It should work. Save multiple plots and line them together manually or you can try comibing geomtile for heatmap generation with facetsgrid for multiple maps of the ggplot2 lib in R.
Cheers
Great suggestions! I will try and tell.
Log in to answer this question.
bit small picture, also this doesn't look like a heatmap. and most important: which data were used to generate this? It's hard to help out of context with contradictory information.
Sorry for my ambigous information. The a larger picture and sample data are attached. It is not a classical heatmap but more like color each point according to its value.