R help - Oct 2015 - Percentage sign in Vegan output

Hi All,

I'm using the Vegan package in R to calculate some variables for my data set
and to make rarefaction curves.
However, I would like to give clear names to my samples and I do not succeed
in this.

For the package, I first read my OTU table (this is a text file with my
samples listed per column. The column header is the sample name as it should
appear in the legend.). After that, I transpose the table for the analysis
and I run the script.
I do get a nice output, meaning my figure looks good and everything. The
only problem is the sample names in the legend. What I have noticed is that
everything after a 'space' is automatically cut off/deleted and that
special
characters are not taken into account. For example, when I want to show 95%,
it gives 95. as an output. Characters like %, /, # are changed into a .
symbol. I was wondering how I can solve this issue, because I would like to
insert spaces and special characters in my sample names.

For example, if I want my sample name to be DNA 95%, how do I have to do
this?

Many thanks in advance!



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On Oct 12, 2015, at 2:08 AM, gktahon wrote:
> Hi All,
> 
> I'm using the Vegan package in R to calculate some variables for my
data set
> and to make rarefaction curves.
> However, I would like to give clear names to my samples and I do not
succeed
> in this.
> 
> For the package, I first read my OTU table (this is a text file with my
> samples listed per column. The column header is the sample name as it
should
> appear in the legend.). After that, I transpose the table for the analysis
> and I run the script.
> I do get a nice output, meaning my figure looks good and everything. The
> only problem is the sample names in the legend. What I have noticed is that
> everything after a 'space' is automatically cut off/deleted and
that special
> characters are not taken into account. For example, when I want to show
95%,
> it gives 95. as an output. Characters like %, /, # are changed into a .
> symbol. I was wondering how I can solve this issue, because I would like to
> insert spaces and special characters in my sample names.
> 
You can turn off the automatic coercion of header text to valid R symbol names,
but then you will then need to always quote them. Read the help page for
`?read.table`

You could use readLines to pull in a single text line for use in annotation.

> For example, if I want my sample name to be DNA 95%, how do I have to do
> this?
Giving a specific response is hampered by the lack of any example code or data.
> 
> Many thanks in advance!
> 
> 
> 
> --
> View this message in context:
http://r.789695.n4.nabble.com/Percentage-sign-in-Vegan-output-tp4713496.html
> Sent from the R help mailing list archive at Nabble.com.
> 
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David Winsemius
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