[R] How to save Results in svg format

Spencer Graves @pencer@gr@ve@ @end|ng |rom e||ect|vede|en@e@org
Fri Dec 4 09:54:52 CET 2020

	  I often have trouble with font sizes in the svg files, because they 
rarely are the same as what I see on the screen.  I then have to read 
the documentation for "par" and play with the cex, cex.axis, cex.lab, 
cex.main, and cex.sub parameters until I get what I want in the svg 
file.  I may also need to play with the "mar" argument in "par". 
Occasionally, I may also have to research some of the other plot 

	  In some cases, I may also need a png file.  I can use "png" in the 
same way as "svg", but the cex, etc., parameters must be set 
differently.  I've recently learned how to open an svg file in the free 
open-source software GIMP and adjust the "Resolution" from the 90 
pixels/in default to something more like 300 to get what I want.  I 
couldn't import an svg file recently into a Google Doc.  The 90 pixels 
per inch default conversion didn't look very clean and sharp after 
imported into a Google Doc.  I tried 600 pixels/in and found that Google 
Doc looked like it accepted it at first.  However, when I went back 
later, I found that it had subsequently malfunctioned.  I tried 300 
pixels/in, and I think that worked, though I'm not 100% certain.

	  hope this helps.
	  Spencer Graves

On 2020-12-03 23:21, David Carlson wrote:
> If you look at the examples on the manual pages for the upgma() and NJ()
> functions you will see that the results are generally sent to the plot()
> function. To save that graph as an .svg file you need to open a graphics
> device using the svg() function, plot the data, and close the graphics
> device. You probably need something like the following:
> svg("UPGMA_5x5.svg")
> plot(UPGMA_5x5)
> dev.off()
> or
> svg("NJ_119x119.svg")
> plot(NJ_119x119)
> dev.off()
> There are numerous arguments that set various details for the plot that you
> should look at (?svg).
> David L Carlson
> Texas A&M University
> On Thu, Dec 3, 2020 at 10:24 PM Anas Jamshed <anasjamshed1994 using gmail.com>
> wrote:
>> #Loading the required libraries
>> library(ape)
>> library(phangorn)
>> library(seqinr)
>> #Importing the required file
>> align_5 <- read.alignment("C:/Users/VAMSI/align 5.fasta", format = "fast")
>> align_119 <- read.alignment("C:/Users/VAMSI/align 119.fasta", format =
>> "fasta")
>> Computing the distance matrix for both UPGMA and NJ algorithms
>> implementation.
>>   matrix_5x5 <- dist.alignment(align_5, matrix = "identity")
>> summary(matrix_5x5)
>> matrix_119x119 <- dist.alignment(align_119, matrix = "identity")
>> summary(matrix_119x119)
>> #Implementation of UPGMA algorithm for a small matrix (5x5) and entire
>> matrix (119x119)
>> UPGMA_5x5 <- upgma(matrix_5x5)
>> UPGMA_119x119 <- upgma(matrix_119x119)
>> summary(UPGMA_5x5)
>> summary(UPGMA_119x119)
>> #Implementation of NJ algorithm for a small matrix (5x5) and entire
>> matrix (119x119)
>> NJ_5x5 <- NJ(matrix_5x5)
>> NJ_119x119 <- NJ(matrix_119x119)
>> summary(NJ_5x5)
>> summary(NJ_119x119)
>> I have done this whole analysis but don't know how can I  the save my
>> tree file in svg or some other image format . In the avove script , I
>> am applying the phylogenetic algorithm on the distance matrix which I
>> have created through fasta file
>>          [[alternative HTML version deleted]]
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> 	[[alternative HTML version deleted]]
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