the first name of the first column

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the first name of the first column

greg holly
Dear all;

I need to run heatmap. Because my first column in my data is alphanumeric,
I can not run as.matrix(scale(my_data)). So I need to make my data readable
as in data(mtcars). In *mtcars *data the first column is alphanumeric and
has no  name.

Thanks,

Greg

        [[alternative HTML version deleted]]

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Re: the first name of the first column

Bert Gunter-2
Clarification needed.

Are your data in a data frame or an alphanumeric matrix? What does it look
like?

A small reproducible example would be very useful here I think!


[1] http://stackoverflow.com/questions/5963269/how-to-make-a-
great-r-reproducible-example
[2] http://adv-r.had.co.nz/Reproducibility.html

Also, is this relevant:

> d <- matrix(1:12,ncol = 4)
> d
     [,1] [,2] [,3] [,4]
[1,]    1    4    7   10
[2,]    2    5    8   11
[3,]    3    6    9   12
> dd <- d[,c(3,1,2,4)]
> dd
     [,1] [,2] [,3] [,4]
[1,]    7    1    4   10
[2,]    8    2    5   11
[3,]    9    3    6   12

Perhaps you neeed to spend time with an R tutorial that covers indexing of
data frames and matrices, an absolutely basic R operation? (I am not clear
from your question if this is your problem).


Cheers,
Bert



Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Thu, May 10, 2018 at 2:36 PM, greg holly <[hidden email]> wrote:

> Dear all;
>
> I need to run heatmap. Because my first column in my data is alphanumeric,
> I can not run as.matrix(scale(my_data)). So I need to make my data readable
> as in data(mtcars). In *mtcars *data the first column is alphanumeric and
> has no  name.
>
> Thanks,
>
> Greg
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
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Re: the first name of the first column

MacQueen, Don
In reply to this post by greg holly
I think you are confusing row names with the first column. The first column in mtcars is not alphanumeric:

> class(mtcars)
[1] "data.frame"
> class(mtcars[,1])
[1] "numeric"

> rownames(mtcars)
 [1] "Mazda RX4"           "Mazda RX4 Wag"       "Datsun 710"          "Hornet 4 Drive"      "Hornet Sportabout"   "Valiant"            (etc)

Perhaps you should make a copy of my_data that includes only the numeric columns?

-Don
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
Lab cell 925-724-7509
 
 
On 5/10/18, 2:36 PM, "R-help on behalf of greg holly" <[hidden email] on behalf of [hidden email]> wrote:

    Dear all;
   
    I need to run heatmap. Because my first column in my data is alphanumeric,
    I can not run as.matrix(scale(my_data)). So I need to make my data readable
    as in data(mtcars). In *mtcars *data the first column is alphanumeric and
    has no  name.
   
    Thanks,
   
    Greg
   
    [[alternative HTML version deleted]]
   
    ______________________________________________
    [hidden email] mailing list -- To UNSUBSCRIBE and more, see
    https://stat.ethz.ch/mailman/listinfo/r-help
    PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    and provide commented, minimal, self-contained, reproducible code.
   

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: the first name of the first column

MacQueen, Don
In reply to this post by greg holly
And more helpful, probably, would have been the str() function:

> str(mtcars)
'data.frame': 32 obs. of  11 variables:
 $ mpg : num  21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ...
 $ cyl : num  6 6 4 6 8 6 8 4 4 6 ...
 $ disp: num  160 160 108 258 360 ...
 $ hp  : num  110 110 93 110 175 105 245 62 95 123 ...
 $ drat: num  3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ...
 $ wt  : num  2.62 2.88 2.32 3.21 3.44 ...
 $ qsec: num  16.5 17 18.6 19.4 17 ...
 $ vs  : num  0 0 1 1 0 1 0 1 1 1 ...
 $ am  : num  1 1 1 0 0 0 0 0 0 0 ...
 $ gear: num  4 4 4 3 3 3 3 4 4 4 ...
 $ carb: num  4 4 1 1 2 1 4 2 2 4 ...

Try it on your data.

-Don

--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
Lab cell 925-724-7509
 
 
On 5/10/18, 2:36 PM, "R-help on behalf of greg holly" <[hidden email] on behalf of [hidden email]> wrote:

    Dear all;
   
    I need to run heatmap. Because my first column in my data is alphanumeric,
    I can not run as.matrix(scale(my_data)). So I need to make my data readable
    as in data(mtcars). In *mtcars *data the first column is alphanumeric and
    has no  name.
   
    Thanks,
   
    Greg
   
    [[alternative HTML version deleted]]
   
    ______________________________________________
    [hidden email] mailing list -- To UNSUBSCRIBE and more, see
    https://stat.ethz.ch/mailman/listinfo/r-help
    PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    and provide commented, minimal, self-contained, reproducible code.
   

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: the first name of the first column

Bert Gunter-2
In reply to this post by Bert Gunter-2
1. My name is Bert, not Brent;

2. I am not your private consultant -- always cc the list unless you have
good reason not to. I have done that here.

It looks like this is what you want; if so, you really need to go through
an R tutorial or two to learn the basics:

d <-
structure(list(region = structure(c(1L, 1L, 1L, 1L), .Label = "zilan",
class = "factor"),
    Fe_ppmtp = c(8.36, 8.78, 16.52, 42.22), Zn.ppmtp = c(0.44,
    0.58, 2.28, 14.22), Mn_tp = c(6.9, 21.16, 27.58, 34.7), Cu_tp = c(0.5,
    0.24, 0.8, 31.9)), class = "data.frame", row.names = c(NA,
-4L))

> md <- as.matrix(d[,-1])  ## knowledge of indexing is essential in R !
> md
     Fe_ppmtp Zn.ppmtp Mn_tp Cu_tp
[1,]     8.36     0.44  6.90  0.50
[2,]     8.78     0.58 21.16  0.24
[3,]    16.52     2.28 27.58  0.80
[4,]    42.22    14.22 34.70 31.90
> is.numeric(md)
[1] TRUE

## to get rid of the column names:

> dimnames(md)[[2]] <- NULL
> md
      [,1]  [,2]  [,3]  [,4]
[1,]  8.36  0.44  6.90  0.50
[2,]  8.78  0.58 21.16  0.24
[3,] 16.52  2.28 27.58  0.80
[4,] 42.22 14.22 34.70 31.90


Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Thu, May 10, 2018 at 3:13 PM, greg holly <[hidden email]> wrote:

> Brent;
>
> I am sorry. Her is the reproducible data
>
> structure(list(region = structure(c(1L, 1L, 1L, 1L), .Label = "zilan",
> class = "factor"),
>     Fe_ppmtp = c(8.36, 8.78, 16.52, 42.22), Zn.ppmtp = c(0.44,
>     0.58, 2.28, 14.22), Mn_tp = c(6.9, 21.16, 27.58, 34.7), Cu_tp = c(0.5,
>     0.24, 0.8, 31.9)), class = "data.frame", row.names = c(NA,
> -4L))
>
>
> On Fri, May 11, 2018 at 1:10 AM, greg holly <[hidden email]> wrote:
>
>> Hi Brent;
>>
>> Thanks so much, fore writing. It is much appreciated. Here is a small
>> example from my data
>>
>> Bolge Fe_ppmtp Zn ppmtp Mn_tp Cu_tp
>> zilan
>> zilan 8.36 0.44 6.9 0.5
>> zilan 8.78 0.58 21.16 0.24
>> zilan 16.52 2.28 27.58 0.8
>> zilan 42.22 14.22 34.7 31.9
>>
>> On Fri, May 11, 2018 at 12:55 AM, Bert Gunter <[hidden email]>
>> wrote:
>>
>>> Clarification needed.
>>>
>>> Are your data in a data frame or an alphanumeric matrix? What does it
>>> look like?
>>>
>>> A small reproducible example would be very useful here I think!
>>>
>>>
>>> [1] http://stackoverflow.com/questions/5963269/how-to-make-a-gre
>>> at-r-reproducible-example
>>> [2] http://adv-r.had.co.nz/Reproducibility.html
>>>
>>> Also, is this relevant:
>>>
>>> > d <- matrix(1:12,ncol = 4)
>>> > d
>>>      [,1] [,2] [,3] [,4]
>>> [1,]    1    4    7   10
>>> [2,]    2    5    8   11
>>> [3,]    3    6    9   12
>>> > dd <- d[,c(3,1,2,4)]
>>> > dd
>>>      [,1] [,2] [,3] [,4]
>>> [1,]    7    1    4   10
>>> [2,]    8    2    5   11
>>> [3,]    9    3    6   12
>>>
>>> Perhaps you neeed to spend time with an R tutorial that covers indexing
>>> of data frames and matrices, an absolutely basic R operation? (I am not
>>> clear from your question if this is your problem).
>>>
>>>
>>> Cheers,
>>> Bert
>>>
>>>
>>>
>>> Bert Gunter
>>>
>>> "The trouble with having an open mind is that people keep coming along
>>> and sticking things into it."
>>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>>>
>>> On Thu, May 10, 2018 at 2:36 PM, greg holly <[hidden email]>
>>> wrote:
>>>
>>>> Dear all;
>>>>
>>>> I need to run heatmap. Because my first column in my data is
>>>> alphanumeric,
>>>> I can not run as.matrix(scale(my_data)). So I need to make my data
>>>> readable
>>>> as in data(mtcars). In *mtcars *data the first column is alphanumeric
>>>> and
>>>> has no  name.
>>>>
>>>> Thanks,
>>>>
>>>> Greg
>>>>
>>>>         [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide http://www.R-project.org/posti
>>>> ng-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>
>>>
>>
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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