[R] heatmap/image from csv data

[David Winsemius]

On Dec 10, 2009, at 10:19 AM, Liat wrote:

>
> I have looked at the help for data.matrix. But didn't find a solution.
> data.matrix only gets two arguments the data and a logical  
> rownames.force -
> I have tried to change this logical to TRUE but that doesn't help.
> Any advice would be greatly appreciated.
> Thanks!!

I interpreted your request as wanting rownames and rownames.force=TRUE  
gives them to you, but ... you wanted the "a" column to be excluded  
from the data and to become the rownames? (You did not actually loose  
those rownames, but you got the coerced result on what was probably a  
factor variable. So, no reproducible data leads again to mis-targeted  
advice. Next time use dput.)

Assuming tst is your dataset name, then try:
 > tmtx <- data.matrix(tst[,-1])
 > rownames(tmtx) <- tst[,1]
 >
 > tmtx
   b c d e
A 1 1 1 1
B 1 0 1 1
C 0 1 0 1
D 1 1 1 0
E 1 0 0 0


>
> Liat wrote:
>>
>> Hi all,
>> I'm trying to use heat.map to display some data.
>> The data is originally in csv format and when I read it in R using
>> read.table I get:
>>  a b c d e
>> 1 A 1 1 1 1
>> 2 B 1 0 1 1
>> 3 C 0 1 0 1
>> 4 D 1 1 1 0
>> 5 E 1 0 0 0
>> The problem is, that for heatmap I need a numerical matrix. When  
>> using
>> data.matrix I get:
>>     a b c d e
>> [1,] 1 1 1 1 1
>> [2,] 2 1 0 1 1
>> [3,] 3 0 1 0 1
>> [4,] 4 1 1 1 0
>> [5,] 5 1 0 0 0
>> So I get numerical... but I loss the row names. I would like to see  
>> these
>> names as the y axis labels.
>> What is the correct/easiest way of achieving this?
>> Many thanks!!!
>>
>
> -- 
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT