ggplot2 reorder factors for faceting
Hi:
(1) Here is one way to reorganize the levels of a factor:
plotData[['infection']] <- factor(plotData[['infection']],
levels = c('InfA', 'InfC', 'InfB', 'InfD'))
Do this ahead of the call to ggplot(), preferably after plotData is defined.
relevel() resets the baseline category of a factor, but here you want
to make multiple changes.
(2) You probably want a better title for the legend. Assuming you want
'Scale' as the title, you can add the following to labs:
labs(..., fill = 'Scale')
HTH,
Dennis
On Tue, Nov 8, 2011 at 3:51 AM, Iain Gallagher
<iaingallagher at btopenworld.com> wrote:
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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