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Small Sandy (NHS Greater Glasgow & Clyde)

2011-Jan-18 09:46 UTC

[R] ggplot2, geom_hline and facet_grid

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

********************************************************************************************************************

This message may contain confidential information. If yo...{{dropped:21}}

Small Sandy (NHS Greater Glasgow & Clyde)

2011-Jan-18 13:51 UTC

head link

[R] ggplot2, geom_hline and facet_grid

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

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

********************************************************************************************************************

This message may contain confidential information. If yo...{{dropped:21}}

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Sandy Small

2011-Jan-19 10:57 UTC

head link

[R] ggplot2, geom_hline and facet_grid

Having upgraded to R version 2.12.1 I still have the same problem:

The combination of facet_grid and geom_hline produce (for me) 4 panels
of which two are empty of any data or lines (labelled "1" and
"2").
Removing either the facet_grid or the geom_hline  gives me the result I
would then expect.

I have tried forcing the rhythm to be a factor
Anyone have any ideas?

Sandy

Dennis Murphy wrote:

    Hi:

    The attached plot comes from the following code:

    g <- ggplot(data =f, aes(x = (variable_time + fixed_time)/2, y
    variable_time - fixed_time))
    g + geom_point() + geom_hline(yintercept =) + 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=glish_United States.1252
    [2] LC_CTYPE=glish_United States.1252
    [3] LC_MONETARY=glish_United States.1252
    [4] LC_NUMERIC=nbsp;
    [5] LC_TIME=glish_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 <ailto:sandy.small at
nhs.net%22>> 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=exs) + 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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