R help - Dec 2009 - Plot odds ratios on log scale

Hi,

I have the following table of odds ratios (or), lower limits(ll) and upper
limits(ul), which I would like to plot as horizontal lines beginning at the
lower limit, ending at the upper limits and with a dot at the odds ratio on an
x-axis on a log10 scale. The y axis would be the study sites.
>From what I can figure out, it looks like the plotCI function will do
everything except give me an x-axis that is on a log10 scale and I can't get
the logaxis function in the log10 package to work.
Study   or      ll      ul      order
UCSF    0.7     0.55    0.89    1
MDA     0.76    0.71    0.93    2
UK      0.68    0.51    0.89    3
Mayo    0.5     0.28    0.87    4

Thanks for any suggestions!

Terri



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On Dec 21, 2009, at 2:54 PM, Rice, Terri wrote:
> Hi,
>
> I have the following table of odds ratios (or), lower limits(ll) and  
> upper limits(ul), which I would like to plot as horizontal lines  
> beginning at the lower limit, ending at the upper limits and with a  
> dot at the odds ratio on an x-axis on a log10 scale. The y axis  
> would be the study sites.
>
>> From what I can figure out, it looks like the plotCI function will  
>> do everything except give me an x-axis that is on a log10 scale and  
>> I can't get the logaxis function in the log10 package to work.
>
> Study   or      ll      ul      order
> UCSF    0.7     0.55    0.89    1
> MDA     0.76    0.71    0.93    2
> UK      0.68    0.51    0.89    3
> Mayo    0.5     0.28    0.87    4
>
> Thanks for any suggestions!
>
> Terri


Terri,

You can build your own easily, using plot() and then either arrows()  
or segments() to create the CI boundary lines. Just use 'log =
"x"' in
the call to plot to create the log scaled x axis.

Presuming that your data above are contained in a data frame called  
'DF':

 > DF
   Study   or   ll   ul order
1  UCSF 0.70 0.55 0.89     1
2   MDA 0.76 0.71 0.93     2
3    UK 0.68 0.51 0.89     3
4  Mayo 0.50 0.28 0.87     4


# Get the range of values for the x axis
xlim <- with(DF, range(or - ll, or + ul))

 > xlim
[1] 0.05 1.69

# Plot the points. set the range of the x axis and set to log10 scale
plot(order ~ or, data = DF, xlim = xlim, pch = 19, log = "x")

# Add the CI's
with(DF, arrows(or - ll, order, or + ul, order, code = 3, angle = 90))

See ?arrows for help on the options for formatting the lines.

Alternatively, since it appears you are doing a meta-analysis of  
sorts, you might want to look at the metaplot() and forestplot()  
functions in Thomas Lumley's 'rmeta' package on CRAN.

HTH,

Marc Schwartz

Please look at the aedotplot, in which we plot four variables:
A effect, B effect, relative risk, and CI on the relative risk.

It should be easily modified to plot the odds ratios.

## install.packages("HH")  ## if you don't have it yet.

library(aedotplot)
example(aedotplot)