Thanks Dennis Yes the plot you sent was what I was expecting. Unfortunately I do not get the same thing using the same commands whn I try it. I notice that I am using a slightly earlier version of R than you. Given that it worked on the Diamonds data I doubt that this the problem but I will upgrade this evening and see if it makes any difference. Here is my session info:
sessionInfo()
R version 2.11.1 (2010-05-31) i386-redhat-linux-gnu locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets grid methods [8] base other attached packages: [1] ggplot2_0.8.9 reshape_0.8.3 plyr_1.4 proto_0.3-8 Sandy Small Clinical Physicist NHS Forth Valley and NHS Greater Glasgow and Clyde
From: Dennis Murphy [djmuser at gmail.com]
Sent: 18 January 2011 11:41
To: Small Sandy (NHS Greater Glasgow & Clyde)
Subject: Re: [R] ggplot2, geom_hline and facet_grid
Sent: 18 January 2011 11:41
To: Small Sandy (NHS Greater Glasgow & Clyde)
Subject: Re: [R] ggplot2, geom_hline and facet_grid
Hi:
The attached plot comes from the following code:
g <- ggplot(data = df, aes(x = (variable_time + fixed_time)/2, y = variable_time - fixed_time))
g + geom_point() + geom_hline(yintercept = 0) + facet_grid(ecd_rhythm ~ .)
Is this what you were expecting?
> sessionInfo()
R version 2.12.1 Patched (2010-12-18 r53869)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] splines stats graphics grDevices utils datasets grid
[8] methods base
other attached packages:
[1] data.table_1.5.1 doBy_4.2.2 R2HTML_2.2 contrast_0.13
[5] Design_2.3-0 Hmisc_3.8-3 survival_2.36-2 sos_1.3-0
[9] brew_1.0-4 lattice_0.19-17 ggplot2_0.8.9 proto_0.3-8
[13] reshape_0.8.3 plyr_1.4
loaded via a namespace (and not attached):
[1] cluster_1.13.2 digest_0.4.2 Matrix_0.999375-46 reshape2_1.1
[5] stringr_0.4 tools_2.12.1
HTH,
Dennis
On Tue, Jan 18, 2011 at 1:46 AM, Small Sandy (NHS Greater Glasgow & Clyde) <sandy.small at nhs.net<mailto:sandy.small at nhs.net>> wrote:
Hi
I have a long data set on which I want to do Bland-Altman style plots for each rhythm type
Using ggplot2, when I use geom_hline with facet_grid I get an extra set of empty panels.
I can't get it to do it with the "Diamonds" data supplied with the package so here is a (much abbreviated) example:
> lvexs
cvd_basestudy ecd_rhythm fixed_time variable_time
1 CBP05J02 AF 30.9000 29.4225
2 CBP05J02 AF 33.1700 32.0350
3 CBP05J02 AF 32.5700 30.2775
4 CBP05J02 AF 32.0550 33.7275
5 CBP05J02 SINUS 30.9175 28.3475
6 CBP05J02 SINUS 30.5725 29.7450
7 CBP05J02 SINUS 33.0000 31.1550
9 CBP05J02 SINUS 31.8350 30.7000
10 CBP05J02 SINUS 34.0450 33.4800
11 CBP05J02 SINUS 31.3975 29.8150
> qplot((variable_time + fixed_time)/2, variable_time - fixed_time, data=lvexs) + facet_grid(ecd_rhythm ~ .) + geom_hline(yintercept=0)
If I take out the geom_hline I get the plots I would expect.
It doesn't seem to make any difference if I get the mean and difference separately.
Can anyone explain this and tell me how to avoid it (and why does it work with the Diamonds data set?
Any help much appreciated - thanks.
Sandy
Sandy Small
Clinical Physicist
NHS Forth Valley
and
NHS Greater Glasgow and Clyde
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