[BioC] Publication Quality Table in R

[Kevin Coombes]

One possibility is to use xtable to write the results out to an HTML 
file and then manually import that HTML file into (gasp) Microsoft 
Word.... (or OpenOffice if you want to avoid the evil empire)

Sean Davis wrote:
> On Mon, Jun 7, 2010 at 3:09 PM, David Lyon <david_lyon3 at yahoo.com> wrote:
>
>   
>> OK I got it to output latex using the package xtable but how do we print
>> out to jpeg or png?
>>
>>     
>
> This is really beyond the scope of R/Bioconductor.  If you are not familiar
> with latex or html, it will be difficult to use xtable, for example.  I
> would suggest using excel for this task and read up on these other topics at
> your leisure.
>
> Sean
>
> Thanks again
>   
>> "my_frame <- read.table(file="table", header=TRUE, sep="\t");
>>  print(design.table, type="latex")"
>>
>> '% latex table generated in R 2.11.0 by xtable 1.5-6 package
>> % Mon Jun  7 16:03:59 2010
>> \begin{table}[ht]
>> \begin{center}
>> \begin{tabular}{rlrr}
>>  \hline
>>  & Age & poor & near.poor \\
>>  \hline
>> 1 & 65-69 &   8 &   4 \\
>>  2 & 70-74 &  10 &   6 \\
>>  3 & 75-79 &  11 &   7 \\
>>  4 & 80-84 &  12 &   8 \\
>>  5 & $>$85 &  14 &  12 \\
>>   \hline
>> \end{tabular}
>> \end{center}
>> \end{table}
>>
>>
>>
>>
>>
>> ________________________________
>> From: Sean Davis <sdavis2 at mail.nih.gov>
>>
>> Cc: bioconductor at stat.math.ethz.ch
>> Sent: Mon, June 7, 2010 2:08:57 PM
>> Subject: Re: [BioC] Publication Quality Table in R
>>
>>
>>
>>
>>
>>
>>     
>>> Thanks for the pointer Sean
>>>
>>>       
>>>> Looks like xtable is the way to go but from reading the documentation and
>>>>         
>> the articles online it doesnt provide a clear example in my eyes how would
>> one convert from an input file like below into a table figure(jpeg or png)
>> for publication.
>>     
>>>> Thanks again for everyones help.\
>>>>         
>>>
>>>       
>> Hi, David.  Sounds like you will need to read a little on R usage.  A great
>> starting place is here:
>>
>> http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual
>>
>>
>>     
>>>> Input File: tab separated:
>>>> Age    poor     near poor
>>>> 65-69    8    4
>>>> 70-74    10    6
>>>> 75-79    11    7
>>>> 80-84    12    8
>>>>         
>>>>> 85    14    12
>>>>>           
>>>
>>>       
>> See the help for read.table.  If this is a one-off thing, loading into
>> excel and exporting as html might also work.
>>
>> Sean
>>
>>
>>     
>>> ________________________________
>>>       
>>>> From: Sean Davis <sdavis2 at mail.nih.gov>
>>>>         
>>>> Cc: bioconductor at stat.math.ethz.ch
>>>> Sent: Mon, June 7, 2010 1:01:27 PM
>>>> Subject: Re: [BioC] Publication Quality Table in R
>>>>         
>>>
>>>
>>>
>>>
>>>
>>>
>>>       
>>>>>> How do I generate a simple table similar to the following link in R
>>>>>>             
>>>>> http://www.fedstats.gov/policy/publications/wp1fig1_text.html
>>>>>           
>>>>>> Table 1 Poverty status, by age, 2000
>>>>>>             
>>>>>> Does anyone know the exact commands? Apologizies for the newbie
>>>>>>             
>> question .
>>     
>>>> See the xtable package, for instance?
>>>>         
>>>> Sean
>>>>         
>>>
>>>
>>>       
>>       [[alternative HTML version deleted]]
>>     
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>>
>>
>>        [[alternative HTML version deleted]]
>>
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>>     
>
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>
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