#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
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Warning: I have basically no idea what you are doing. I presume that you have consulted ?svg, however. If not , you should probably do so. Also, a search on "save as svg" on rseek.org brought up the svglite package, among other resources. You might want to see what that offers. Cheers, Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Thu, Dec 3, 2020 at 7:12 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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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. >[[alternative HTML version deleted]]
On 12/3/20 7:12 PM, Anas Jamshed 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 formatSVG format is for graphics. I don't see any R graphics calls or anything I recognize as a "tree". (Perhaps the summary function for objects returned from `upgma` include graphics? I surely do not know.) Cairo graphics is supported in the grDevices package. It should be loaded by default. Have your tried this at your console: ?svg -- David.> > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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.