[R] Question about correlation

[Göran Broström]

Please keep the conversation on the list: Others may be able to help you 
better than I can.

On 2017-07-06 10:38, SEB140004 Student wrote:
> Ya. I had successfully got the result. Thank you very much. :)
> 
> Isn't possible for me to obtain the network from the correlation matrix?

I know nothing about correlation networks, but by googling I found two R 
packages, ggraph and corrr, that may be of interest to you.

Göran

> On Thu, Jul 6, 2017 at 1:38 AM, Göran Broström <goran.brostrom at umu.se 
> <mailto:goran.brostrom at umu.se>> wrote:
> 
>     On 2017-07-05 11:56, Jim Lemon wrote:
> 
>         Hi Chin Yi,
>         If you are trying to correlate "Health" with "Disease", i.e.
> 
>         cydf<-read.table(text="OTU ID Health Disease
>             Bacterial 1 0.29 0.34
>             Bacterial 2 0.25 0.07
>             Bacterial 3 0.06 0.06
>             Bacterial 4 0.07 0.09
>             Bacterial 5 0.02 0.05",
>             header=TRUE)
>         print(cor(cydf$Health,cydf$Disease))
>         [1] 0.7103517
> 
>         If you are getting that error, it probably means that either
>         "Health"
>         or "Disease" or perhaps both have been read in as a factor. To test
>         this:
> 
>         is.factor(cydf$Health)
>         [1] FALSE
> 
>             is.factor(cydf$Disease)
> 
>         [1] FALSE
> 
>         If either of these returns TRUE, that is almost certainly the
>         problem.
> 
> 
>     Or maybe Chin Yi tried (as it seems)
> 
>      > cor(cydf)
>     Error in cor(cydf) : 'x' must be numeric
> 
>     (with cydf == data): 'OTU' is not numeric.
> 
>     Follow Jim's advice.
> 
>     Göran
> 
> 
> 
>         Jim
> 
> 
>         On Wed, Jul 5, 2017 at 11:27 AM, SEB140004 Student
>         <chinyi at siswa.um.edu.my <mailto:chinyi at siswa.um.edu.my>> wrote:
> 
>             Greeting.
> 
>             Dear Mr/Mrs/Miss,
> 
>             OTU ID Health Disease
>             Bacterial 1 0.29 0.34
>             Bacterial 2 0.25 0.07
>             Bacterial 3 0.06 0.06
>             Bacterial 4 0.07 0.09
>             Bacterial 5 0.02 0.05
>             Above show the first 6 data sets, may I ask that the reason
>             of R show the
>             error like "Error in cor(data) : 'x' must be numeric" ? And
>             how to solve
>             it? Besides, isn't this data can conduct correlation matrix?
> 
>             Moreover, isn't this data sets can be plot into network? If
>             can, which
>             package should I use?
> 
>             Thank you.
> 
>             Best regards,
>             Kang Chin Yi
> 
>                       [[alternative HTML version deleted]]
> 
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> 
>