File:Ncbi-prok-genomesize.svg
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Summary edit
| Description |
English: Log-log plot of the total number of annotated proteins in bacterial and archeal genomes submitted to GenBank as a function of genome size. Based on data from NCBI genome reports. |
| Date | |
| Source | Own work |
| Author | Estevezj |
| SVG development | |
| Source code | R code#!/usr/bin/Rscript
# File-Name: prok-genomes-genes-graph.R
# Date: 2013-01-11
# Author: James Estevez (User:Estevezj)
# Purpose: This generates a log-log plot of protein count as a function of genome size.
# Data Used: ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/prokaryotes.txt
# License: To the extent possible under law, the author(s) have
# dedicated all copyright and related and neighboring rights to this software to
# the public domain worldwide. This software is distributed without any
# warranty. You should have received a copy of the CC0 Public Domain Dedication
# along with this software. If not, see
# <https://creativecommons.org/publicdomain/zero/1.0/>.
library(grDevices)
library(ggplot2)
library(plyr)
library(taxize)
# Download our tables from NCBI's FTP site. Accessed Fri Jan 11 23:02:49 PST 2013
prok <- read.table("ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/prokaryotes.txt", sep="\t", comment.char="!", header=T, stringsAsFactors = F)
prok <- read.table("ncbi-ftp-reports-prokaryotes.txt", sep="\t", comment.char="!", header=T, stringsAsFactors = F)
# Clear missing values ('-')
prok.cut <- prok[(prok$Size..Mb. != '-') & (prok$Proteins != '-'),]
# Set classes
prok.cut$Size..Mb. <- as.numeric(prok.cut$Size..Mb.)
prok.cut$Proteins <- as.numeric(prok.cut$Proteins)
prok.cut$Group <- as.factor(prok.cut$Group)
# From which domain of life does each genome come?
groups <- levels(prok.cut$Group)
get_domain <- function(x){first.hit <- classification(get_uid(x))[[1]] # return the first hit
kingdom <- as.character(first.hit[which(first.hit[,"Rank"] == "superkingdom"), 1]) # extract domain
return(data.frame(Group = x, Domain = kingdom))
}
domains <- ldply(groups, get_domain)
foo <- prok.cut
prok.cut <- merge(prok.cut, domains, by = "Group")
# Draw our plot
p <- ggplot(prok.cut, aes(Size..Mb., Proteins, color = Domain))
# Save our plot to SVG
svg(filename='ncbi-prok-genomesize.svg', width = 14, height = 8)
p + geom_point(alpha = 0.5, size = 2) +
scale_y_log10() +
scale_x_log10() +
scale_shape(solid = FALSE) +
ggtitle("The total genome size and the number of genes in bacteria and archaea.") +
xlab('Genome size (Megabases)') +
ylab("Number of protein coding genes") +
scale_colour_brewer(type="qual", palette=3)
dev.off()
|
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I, the copyright holder of this work, hereby publish it under the following license:
This file is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.
- 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.
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| Date/Time | Thumbnail | Dimensions | User | Comment | |
|---|---|---|---|---|---|
| current | 07:00, 12 January 2013 | | 1,260 × 720 (917 KB) | Estevezj (talk | contribs) | User created page with UploadWizard |
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