Dear List
I am trying to draw a heatmap using ggplot2. In this heatmap I have faceted my
data by 'infection' of which I have four. These four infections break down into
two types and I would like to reorder the 'infection' column of my data to
reflect this.
Toy example below:
library(ggplot2)
# test data for ggplot reordering
genes <- (rep (c(rep('a',4), rep('b',4), rep('c',4), rep('d',4), rep('e',4),
rep('f',4)) ,4))
fcData <- rnorm(96)
times <- rep(rep(c(2,6,24,48),6),4)
infection <- c(rep('InfA', 24), rep('InfB', 24), rep('InfC', 24), rep('InfD',
24))
infType <- c(rep('M', 24), rep('D',24), rep('M', 24), rep('D', 24))
# data is long format for ggplot2
plotData <- as.data.frame(cbind(genes, as.numeric(fcData), as.numeric(times),
infection, infType))
hp2 <- ggplot(plotData, aes(factor(times), genes)) + geom_tile(aes(fill =
scale(as.numeric(fcData)))) + facet_wrap(~infection, ncol=4)
# set scale
hp2 <- hp2 + scale_fill_gradient2(name=NULL, low="#0571B0", mid="#F7F7F7",
high="#CA0020", midpoint=0, breaks=NULL, labels=NULL, limits=NULL,
trans="identity")
# set up text (size, colour etc etc)
hp2 <- hp2 + labs(x = "Time", y = "") + scale_y_discrete(expand = c(0, 0)) +
opts(axis.ticks = theme_blank(), axis.text.x = theme_text(size = 10, angle =
360, hjust = 0, colour = "grey25"), axis.text.y = theme_text(size=10, colour =
'gray25'))
hp2 <- hp2 + theme_bw()
In the resulting plot I would like infections infA and infC plotted next to
each other and likewise for infB and infD. I have a column in the data -
infType - which I could use to reorder the infection column but so far I have
no luck getting this to work.
Could someone give me a pointer to the best way to reorder the infection factor
and accompanying data into the order I would like?
Best
iain
> sessionInfo()
R version 2.13.2 (2011-09-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.6
loaded via a namespace (and not attached):
[1] digest_0.5.0 tools_2.13.2
>
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