File:Bacterial and archeal genome sequences submitted to Genbank.svg

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Original file ‎(SVG file, nominally 1,350 × 450 pixels, file size: 46 KB)

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Summary

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Description
English: Plot of the total number of prokaryotic genomes submitted to Genbank as a function of time. Based on data from genome reports.
Date
Source Own work
Author Estevezj
SVG development
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Source code
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R code

# Download our tables from NCBI's FTP site. Accessed 14:30PST, 18 December 2012
prok <- read.table("ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/prokaryotes.txt", sep="\t", comment.char="!", header=T)

# Pull release dates, while dropping rows lacking a release date.
prok  <- as.Date(prok$Release.Date[prok$Release.Date != '-'],format="%Y/%m/%d")

# Bin our dates by month and year, tabulate, and save to a dataframe.
prok.cut <- as.data.frame( 
  table(
    as.Date(
      cut(prok, "month")
      )
    )
  )

# Correct our column titles, calculate a running total, and reconvert from factor to date
colnames(prok.cut) <- c("Date", "Total")
prok.cut$Total <- cumsum(prok.cut$Total)
prok.cut$Date <- as.Date(prok.cut$Date)


# Draw our plot
library("ggplot2")
p <- ggplot(prok.cut, aes(Date, Total))


# Save our plot to SVG
library(grDevices)
svg(filename='ncbi-genomes.svg', width = 15, height = 5)
p +  geom_area() +  xlab("") +  ylab("")
# Alternately, with titles
# +  ggtitle("Bacterial and archeal genome sequences submitted to Genbank") + xlab('Time') +  ylab("Total number of genomes")
dev.off()

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I, the copyright holder of this work, hereby publish it under the following license:
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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/TimeThumbnailDimensionsUserComment
current02:00, 19 December 2012Thumbnail for version as of 02:00, 19 December 20121,350 × 450 (46 KB)Estevezj (talk | contribs)added english captions
01:57, 19 December 2012Thumbnail for version as of 01:57, 19 December 20121,350 × 450 (17 KB)Estevezj (talk | contribs)User created page with UploadWizard

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