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Suzanne Matthews

2007-Jul-19 00:07 UTC

[R] help with heatmap - how to remove annoying "X" before numeric values?

Hello All,

I have a simple question based on how things are labeled on my heat map;
particularly, there is this annoying "X" that appears before the
numeric
value of all the labels of my columns.

Let's say I have the following silly data, stored in "temp.txt"
        1905    1910    1950    1992    2011    2020
Gnat    0.08    0.29    0.29    0.37    0.39    0.43
Snake   0.16    0.34    0.32    0.40    0.41    0.53
Bat     0.40    0.54    0.52    0.60    0.60    0.63
Cat     0.16    0.27    0.29    0.39    0.37    0.41
Dog     0.43    0.54    0.52    0.61    0.60    0.62
Lynx    0.50    0.57    0.54    0.59    0.5     0.59

I use the following commands to generate my heatmap:
heat <- read.table('temp.txt')
x <- as.matrix(heat)

heatmap.2(x, keysize=1.2, dendrogram="none", trace="none",
Colv = FALSE,
main = "Silly Data", labColNULL, margin=c(7,8))

This generates a very nice heatmap, but there is one thing I have an issue
with: How do I get rid of the 'X' that seems to come automatically
before my
numeric column values? I just want those columns to be labeled 1905, 1910,
1950, and so on. I cannot find anything in the heatmap.2 documentation that
suggests how I should do this.

Thank you very much for your time, and patience in reading this!

Sincerely,
Suzanne

	[[alternative HTML version deleted]]

Gabor Grothendieck

2007-Jul-19 02:05 UTC

head link

[R] help with heatmap - how to remove annoying "X" before numeric values?

read.table is doing that, not heatmap.2.  Use
   read.table("temp.txt", header = TRUE, check.names = FALSE)

On 7/18/07, Suzanne Matthews <suzanne.j.matthews at gmail.com>
wrote:> Hello All,
>
> I have a simple question based on how things are labeled on my heat map;
> particularly, there is this annoying "X" that appears before the
numeric
> value of all the labels of my columns.
>
> Let's say I have the following silly data, stored in
"temp.txt"
>        1905    1910    1950    1992    2011    2020
> Gnat    0.08    0.29    0.29    0.37    0.39    0.43
> Snake   0.16    0.34    0.32    0.40    0.41    0.53
> Bat     0.40    0.54    0.52    0.60    0.60    0.63
> Cat     0.16    0.27    0.29    0.39    0.37    0.41
> Dog     0.43    0.54    0.52    0.61    0.60    0.62
> Lynx    0.50    0.57    0.54    0.59    0.5     0.59
>
> I use the following commands to generate my heatmap:
> heat <- read.table('temp.txt')
> x <- as.matrix(heat)
>
> heatmap.2(x, keysize=1.2, dendrogram="none",
trace="none", Colv = FALSE,
> main = "Silly Data", labCol> NULL, margin=c(7,8))
>
> This generates a very nice heatmap, but there is one thing I have an issue
> with: How do I get rid of the 'X' that seems to come automatically
before my
> numeric column values? I just want those columns to be labeled 1905, 1910,
> 1950, and so on. I cannot find anything in the heatmap.2 documentation that
> suggests how I should do this.
>
> Thank you very much for your time, and patience in reading this!
>
> Sincerely,
> Suzanne
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> 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.
>

Moshe Olshansky

2007-Jul-19 02:57 UTC

head link

[R] help with heatmap - how to remove annoying "X" before numeric values?

Hi Suzanne,

My solution (which I am sure is not the best) would
be:
> heat <- read.table('temp.txt')
> heat      X1905 X1910 X1950 X1992 X2011 X2020
Gnat   0.08  0.29  0.29  0.37  0.39  0.43
Snake  0.16  0.34  0.32  0.40  0.41  0.53
Bat    0.40  0.54  0.52  0.60  0.60  0.63
Cat    0.16  0.27  0.29  0.39  0.37  0.41
Dog    0.43  0.54  0.52  0.61  0.60  0.62
Lynx   0.50  0.57  0.54  0.59  0.50  0.59> a<-names(heat)
> b<-strsplit(a,split="X")
> w<-unlist(b)
> w [1] ""     "1905" ""     "1910"
""     "1950" ""
"1992" ""     "2011" ""    
"2020"> z <- w[seq(2,length(w),by=2)]
> z[1] "1905" "1910" "1950" "1992"
"2011" "2020"> names(heat) <- z
> heat      1905 1910 1950 1992 2011 2020
Gnat  0.08 0.29 0.29 0.37 0.39 0.43
Snake 0.16 0.34 0.32 0.40 0.41 0.53
Bat   0.40 0.54 0.52 0.60 0.60 0.63
Cat   0.16 0.27 0.29 0.39 0.37 0.41
Dog   0.43 0.54 0.52 0.61 0.60 0.62
Lynx  0.50 0.57 0.54 0.59 0.50 0.59> 
Regards,

Moshe.

--- Suzanne Matthews <suzanne.j.matthews at gmail.com>
wrote:
> Hello All,
> 
> I have a simple question based on how things are
> labeled on my heat map;
> particularly, there is this annoying "X" that
> appears before the numeric
> value of all the labels of my columns.
> 
> Let's say I have the following silly data, stored in
> "temp.txt"
>         1905    1910    1950    1992    2011    2020
> Gnat    0.08    0.29    0.29    0.37    0.39    0.43
> Snake   0.16    0.34    0.32    0.40    0.41    0.53
> Bat     0.40    0.54    0.52    0.60    0.60    0.63
> Cat     0.16    0.27    0.29    0.39    0.37    0.41
> Dog     0.43    0.54    0.52    0.61    0.60    0.62
> Lynx    0.50    0.57    0.54    0.59    0.5     0.59
> 
> I use the following commands to generate my heatmap:
> heat <- read.table('temp.txt')
> x <- as.matrix(heat)
> 
> heatmap.2(x, keysize=1.2, dendrogram="none",
> trace="none", Colv = FALSE,
> main = "Silly Data", labCol> NULL, margin=c(7,8))
> 
> This generates a very nice heatmap, but there is one
> thing I have an issue
> with: How do I get rid of the 'X' that seems to come
> automatically before my
> numeric column values? I just want those columns to
> be labeled 1905, 1910,
> 1950, and so on. I cannot find anything in the
> heatmap.2 documentation that
> suggests how I should do this.
> 
> Thank you very much for your time, and patience in
> reading this!
> 
> Sincerely,
> Suzanne
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> 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.
>

Suzanne Matthews

2007-Jul-19 16:14 UTC

head link

[R] help with heatmap - how to remove annoying "X" before numeric values?

Sorry, I just realized I didn't send this to the list! (See below)

Thanks for all the help! All is working fine now.

If anyone knows of a more straightforward way to change the "Value"
string
for the Key, please let me know (just to satisfy my curiosity).  I got it to
work by modifying the source code (specifically, "heatmap.2.R " in the
gplots package).

However, before, I didn't make the call
source("heatmap.2.R")

before I called
source("mysillyheatmap.R")

Making the additional call to " heatmap.2.R" fixed everything.

Thanks again for all your help!



On 7/19/07, Suzanne Matthews <suzanne.j.matthews@gmail.com>
wrote:>
> Thank you all for your prompt replies! The check.names=FALSE parameter
> fixed things entirely.
>
> One more question:
>
> Is there a straightforward way to modify the the "Values" string
that
> labels the key to a user-defined value? For example, let's say I want
to
> change "Values" to "Silly Values". So far, what I have
found that I need to
> do is actually go and change a static string in the source code. Is there a
> more direct way?
>
> Also, after I make the source code change (in gplots package, file:
> heatmap.2.R), how do I have R build from that? If I remember correctly, if
> I put the new heatmap.2.R in my directory, R is supposed to check for
> functions and such there before it goes and builds it from the main source
> code base (located at /usr/bin/R). I am a touch confused on which directory
> is "my" directory, where R will check first. I tried putting the
modified
> heatmap.2.R file in the directory that my script is, and where I initially
> run R. But that didn't work!
>
> Is there anything that I should add to my R script that will force it to
> read from that from my directory? If not, which directory should I place
> this in?
>
> My OS is OS X, so I think Unix-based instructions will work.
>
> Thank you once again for your time and patience!
>
> Sincerely,
> Suzanne
>
> On 7/18/07, Moshe Olshansky <m_olshansky@yahoo.com> wrote:
> >
> > I was right saying that my solution was not the best
> > possible!
> >
> > --- Prof Brian Ripley <ripley@stats.ox.ac.uk> wrote:
> >
> > > read.table('temp.txt', check.names = FALSE)
> > >
> > > would be easier (and more general, since make.names
> > > can do more than
> > > prepend an 'X').
> > >
> > > On Wed, 18 Jul 2007, Moshe Olshansky wrote:
> > >
> > > > Hi Suzanne,
> > > >
> > > > My solution (which I am sure is not the best)
> > > would
> > > > be:
> > > >
> > > >> heat <- read.table('temp.txt')
> > > >> heat
> > > >      X1905 X1910 X1950 X1992 X2011 X2020
> > > > Gnat   0.08  0.29  0.29  0.37  0.39  0.43
> > > > Snake  0.16  0.34  0.32  0.40  0.41  0.53
> > > > Bat    0.40  0.54  0.52  0.60  0.60  0.63
> > > > Cat    0.16  0.27  0.29  0.39  0.37  0.41
> > > > Dog    0.43  0.54  0.52  0.61  0.60  0.62
> > > > Lynx   0.50  0.57  0.54  0.59  0.50  0.59
> > > >> a<-names(heat)
> > > >> b<-strsplit(a,split="X")
> > > >> w<-unlist(b)
> > > >> w
> > > > [1] ""     "1905" ""    
"1910" ""     "1950" ""
> > > > "1992" ""     "2011"
""     "2020"
> > > >> z <- w[seq(2,length(w),by=2)]
> > > >> z
> > > > [1] "1905" "1910" "1950"
"1992" "2011" "2020"
> > > >> names(heat) <- z
> > > >> heat
> > > >      1905 1910 1950 1992 2011 2020
> > > > Gnat  0.08 0.29 0.29 0.37 0.39 0.43
> > > > Snake 0.16 0.34 0.32 0.40 0.41 0.53
> > > > Bat   0.40 0.54 0.52 0.60 0.60 0.63
> > > > Cat   0.16 0.27 0.29 0.39 0.37 0.41
> > > > Dog   0.43 0.54 0.52 0.61 0.60 0.62
> > > > Lynx  0.50 0.57 0.54 0.59 0.50 0.59
> > > >>
> > > >
> > > > Regards,
> > > >
> > > > Moshe.
> > > >
> > > > --- Suzanne Matthews
> > > <suzanne.j.matthews@gmail.com>
> > > > wrote:
> > > >
> > > >> Hello All,
> > > >>
> > > >> I have a simple question based on how things are
> > > >> labeled on my heat map;
> > > >> particularly, there is this annoying "X" that
> > > >> appears before the numeric
> > > >> value of all the labels of my columns.
> > > >>
> > > >> Let's say I have the following silly data, stored
> > > in
> > > >> "temp.txt"
> > > >>         1905    1910    1950    1992    2011
> > > 2020
> > > >> Gnat    0.08    0.29    0.29    0.37    0.39
> > > 0.43
> > > >> Snake   0.16    0.34    0.32    0.40    0.41
> > > 0.53
> > > >> Bat     0.40    0.54    0.52    0.60     0.60
> > > 0.63
> > > >> Cat     0.16    0.27    0.29    0.39    0.37
> > > 0.41
> > > >> Dog     0.43    0.54    0.52    0.61    0.60
> > > 0.62
> > > >> Lynx    0.50    0.57    0.54    0.59     0.5
> > > 0.59
> > > >>
> > > >> I use the following commands to generate my
> > > heatmap:
> > > >> heat <- read.table('temp.txt')
> > > >> x <- as.matrix(heat)
> > > >>
> > > >> heatmap.2(x, keysize=1.2, dendrogram="none",
> > > >> trace="none", Colv = FALSE,
> > > >> main = "Silly Data", labCol> > >
>> NULL, margin=c(7,8))
> > > >>
> > > >> This generates a very nice heatmap, but there is
> > > one
> > > >> thing I have an issue
> > > >> with: How do I get rid of the 'X' that seems to
> > > come
> > > >> automatically before my
> > > >> numeric column values? I just want those columns
> > > to
> > > >> be labeled 1905, 1910,
> > > >> 1950, and so on. I cannot find anything in the
> > > >> heatmap.2 documentation that
> > > >> suggests how I should do this.
> > > >>
> > > >> Thank you very much for your time, and patience
> > > in
> > > >> reading this!
> > > >>
> > > >> Sincerely,
> > > >> Suzanne
> > > >>
> > > >>    [[alternative HTML version deleted]]
> > > >>
> > > >> ______________________________________________
> > > >> R-help@stat.math.ethz.ch mailing list
> > > >> 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.
> > > >>
> > > >
> > > > ______________________________________________
> > > > R-help@stat.math.ethz.ch mailing list
> > > > 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.
> > > >
> > >
> > > --
> > > Brian D. Ripley,
> > > ripley@stats.ox.ac.uk
> > > Professor of Applied Statistics,
> > >
http://www.stats.ox.ac.uk/~ripley/<http://www.stats.ox.ac.uk/%7Eripley/>
> > > University of Oxford,             Tel:  +44 1865
> > > 272861 (self)
> > > 1 South Parks Road,                     +44 1865
> > > 272866 (PA)
> > > Oxford OX1 3TG, UK                Fax:  +44 1865
> > > 272595
> > >
> >
> >
>
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