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Summary
| 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 | |
| Source code | 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()
|
Licensing
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.
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File history
Click on a date/time to view the file as it appeared at that time.
| Date/Time | Thumbnail | Dimensions | User | Comment | |
|---|---|---|---|---|---|
| current | 02:00, 19 December 2012 | | 1,350 × 450 (46 KB) | Estevezj | added english captions |
| 01:57, 19 December 2012 |  | 1,350 × 450 (17 KB) | Estevezj | User created page with UploadWizard |
File usage
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