How to save Results in svg format
Another option is to open the svg file in Inkscape which is a vector-based
editor. If you are planning to do this and work with the text labels, it is
easier to use svglite() in the package of the same name which draws text as
characters that can be selected and edited more easily than in files saved
with svg(). To see the difference look at the following files in a plain
text editor:
svg("Test.svg")
plot(0:1, 0:1, axes=FALSE, pch="", xlab="", ylab="")
text(.5, .5, "HELLO", cex=5)
dev.off()
library(svglite)
svglite("Testlite.svg")
plot(0:1, 0:1, axes=FALSE, pch="", xlab="", ylab="")
text(.5, .5, "HELLO", cex=5)
dev.off()
David L Carlson
On Fri, Dec 4, 2020 at 2:55 AM Spencer Graves <
spencer.graves at effectivedefense.org> wrote:
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
parameters.
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 at 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
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