[R] Plot odds ratios on log scale

[Marc Schwartz]

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