File:Citrus tern cb simplified.svg
Original file (SVG file, nominally 899 × 911 pixels, file size: 121 KB)
Captions
Captions
Summary[edit]
| Description |
English: Citrus fruits clustered by genetic similarity of partial sequences. Ternary diagram showing hybridization in citrus cultivars. Data from (2014-12). "Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrusspecies: analysis of chromosome 2". BMC Genetics 15 (1). DOI:10.1186/s12863-014-0152-1. ISSN 1471-2156. Retrieved on 2017-07-08. |
| Date | |
| Source | Own work |
| Author | HLHJ |
| Other versions | File:Citrus_tern_cb_simplified_1.svg (updated version using full, not partial, sequences) This version should be used. The original paper plots a slightly extended version of this superseded dataset in 3-D, see File:S12863-014-0152-1-3.gif. |
 | This page is presently inactive and retained primarily for historical interest.
If you want to revive discussion regarding the subject, you may try using the talk page (though your voice may not be heard) or start a discussion at the Village pump. |
Licensing[edit]
- You are free:
- to share – to copy, distribute and transmit the work
- to remix – to adapt the work
- Under the following conditions:
- attribution – You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
- share alike – If you remix, transform, or build upon the material, you must distribute your contributions under the same or compatible license as the original.
Derivation[edit]
This diagram was made using the Unix command line, the statistics language R, and the SVG editor Inkscape, using the following algorithm. Use "Edit" to get it with newlines, and thus formatted so you can cut-and-paste it.
Script for making the diagram from the raw data[edit]
#Data from Additional file 8, Curk et al., "Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrus species: analysis of chromosome 2" BMC Genetics 2014 15:152, doi:10.1186/s12863-014-0152-1
#Copy-and-paste pdf's table to an ASCII text file, citrus_tern_table.txt
#Remove the error estimates by removing all lines beginning with '±'
cat citrus_tern_table.txt | sed '/^±/ d' > citrus_tern_table2.txt
#Remove blank lines
cat citrus_tern_table2.txt | sed '/^$/ d' > citrus_tern_table3.txt
#Because sed reads things line-by-line, replacing patterns containing newlines (\n0 with \t0, in this case) is awkward.
#Thanks http://stackoverflow.com/questions/1251999/how-can-i-replace-a-newline-n-using-sed?noredirect=1
cat citrus_tern_table3.txt | sed -e ':a' -e 'N' -e '$!ba' -e 's/\n0/\t0/g' > citrus_tern_table4.txt
#Add a leading newline back, so you get a leading tab
echo -e | cat - citrus_tern_table4.txt > citrus_tern_table5.txt
#Replace the newlines in the header with tabs
cat citrus_tern_table5.txt | sed -e ':a' -e 'N' -e '$!ba' -e 's/\nC\. /\tC\./g' > citrus_tern_table_done.txt
#Manually took out a random newline in "Deep Red [\n]pummelo"
#Manually changed Meyer lemo -> Meyer lemon
#Manually changed Nanfengmijuu -> Nanfengmiju
#Enter R command-line environment
R
#Load needed library. If fails, may need to run this: install.packages("ggtern")
library(ggtern)
#read datatable and tidy format
citrus_table = read.csv("./citrus_tern_table_done.txt",header=TRUE, sep = "\t")
dimnames(citrus_table)1<-citrus_table[,1]
citrus_table[,1] <- NULL
#====================================================================
#Make an original theme that works for colourblind viewers
#See http://bconnelly.net/2013/10/creating-colorblind-friendly-figures/
colours_colourblind<-c("black"="#000000", "cb_orange"="#E69F00", "cb_pale_blue"="#56B4E9", "cb_green"="#009E73", "cb_yellow"="#F0E442", "cb_darkblue"="#0072B2", "cb_red"="#D55E00", "cb_purple"="#CC79A7")
theme_colourblind<-theme_custom(base_size = 12, base_family = "", tern.plot.background = NULL, tern.panel.background = "grey92", col.T = colours_colourblind[2], col.L = colours_colourblind[6], col.R = colours_colourblind[7], col.grid.minor = "white")
#====================================================================
#Basic plot using built-in theme, not too good for colourblind viewers, for debugging
#citrus_tern <- ggtern(data = citrus_table, aes(x = C.maxima, y = C.reticulata, z = C.medica)) +geom_point(size = 4, shape = 21, color = "black") + ggtitle("Citrus hybrids") + theme_gray() + theme(legend.position = c(0,1), legend.justification = c(0, 1)) +geom_text(aes(label=rownames(citrus_table)),hjust=0, vjust=0)
#Plot that works for colourblind viewers,
citrus_tern <- ggtern(data = citrus_table, aes(x = C.maxima, y = C.reticulata, z = C.medica)) +geom_point(size = 4, shape = 21, color = "black") + ggtitle("Citrus hybrids") + theme_colourblind + theme(legend.position = c(0,1), legend.justification = c(0, 1)) +geom_text(aes(label=rownames(citrus_table)),hjust=0, vjust=0)
citrus_tern
#====================================================================
#Output plot as an svg file
svg("citrus_tern.svg",width=10,height=10)
citrus_tern
dev.off()
#Prettify. Manually edit labels, titles, etc. using the Inkscape SVG editor
File history
Click on a date/time to view the file as it appeared at that time.
| Date/Time | Thumbnail | Dimensions | User | Comment | |
|---|---|---|---|---|---|
| current | 01:10, 9 July 2017 | | 899 × 911 (121 KB) | HLHJ (talk | contribs) | Distinguishes between lemons (asexually propagated bud sport group), and recent independent hybrids, now labeled ''Brand "lemon"'' rather than ''Brand lemon''. |
| 16:45, 8 July 2017 |  | 899 × 911 (119 KB) | HLHJ (talk | contribs) | User created page with UploadWizard |
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