Re: [R] 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.gra...@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 University > > > > > > On Thu, Dec 3, 2020 at 10:24 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 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]] > >> > >> __ > >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > >> > >> > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-help__;!!KwNVnqRv!T-8PRCLc041aD-rW1ehtb14tfQAVpWdpBddf_q6Raeho0RbG9wDodEK_QDpGMCc$ > >> PLEASE do read the posting guide > >> > https://urldefense.com/v3/__http://www.R-project.org/posting-guide.html__;!!KwNVnqRv!T-8PRCLc041aD-rW1ehtb14tfQAVpWdpBddf_q6Raeho0RbG9wDodEK_1H9sJRs$ > >> and provide commented, minimal, self-contained, reproducible code. > >> > > > > [[alternative HTML version deleted]] > > > > __ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > >
Re: [R] How to save Results in svg format
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 University On Thu, Dec 3, 2020 at 10:24 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 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]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-help__;!!KwNVnqRv!T-8PRCLc041aD-rW1ehtb14tfQAVpWdpBddf_q6Raeho0RbG9wDodEK_QDpGMCc$ PLEASE do read the posting guide https://urldefense.com/v3/__http://www.R-project.org/posting-guide.html__;!!KwNVnqRv!T-8PRCLc041aD-rW1ehtb14tfQAVpWdpBddf_q6Raeho0RbG9wDodEK_1H9sJRs$ and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@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. __ R-help@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.
Re: [R] How to save Results in svg format
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 University On Thu, Dec 3, 2020 at 10:24 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 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]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-help__;!!KwNVnqRv!T-8PRCLc041aD-rW1ehtb14tfQAVpWdpBddf_q6Raeho0RbG9wDodEK_QDpGMCc$ > PLEASE do read the posting guide > https://urldefense.com/v3/__http://www.R-project.org/posting-guide.html__;!!KwNVnqRv!T-8PRCLc041aD-rW1ehtb14tfQAVpWdpBddf_q6Raeho0RbG9wDodEK_1H9sJRs$ > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@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.