Plotting SRA database growth

The Sequence Read Archive is NCBI’s database for high throughput sequencing data and the largest public repository for such data.
The data on the growth of the database is available here

Load packages

suppressPackageStartupMessages(library(magrittr))
suppressPackageStartupMessages(library(httr))
suppressPackageStartupMessages(library(ggplot2))

Function to make nicer axis labels

scientific_10 <- function(x) {
  xx <- dplyr::case_when(x>=0 & x<=100 ~ as.character(x),
                         x>100 & log10(x)%%1==0 ~ gsub(".+e\\+", "10^", scales::scientific_format()(x)),
                         TRUE ~ gsub("e\\+", " %*% 10^", scales::scientific_format()(x))) 
  parse(text = xx)
}

Download the data in R

sraurl <- "https://www.ncbi.nlm.nih.gov/Traces/sra/sra_stat.cgi"

sra <- httr::GET(url=sraurl) %>% 
        httr::content(encoding="UTF-8")

sra$date <- as.Date(sra$date, format = "%m/%d/%Y")

Plot with linear scale

sra %>%
  dplyr::select(date, bases, open_access_bases) %>%
  tidyr::pivot_longer(cols = 2:3, names_to = "type", values_to = "terabases") %>%
  dplyr::mutate(terabases = terabases / 1e12) %>%
  dplyr::mutate(type = dplyr::case_when(type == "bases" ~ "total bases",
                                 type == "open_access_bases" ~ "open access bases")) %>%
ggplot(mapping = aes(x = date, y = terabases, color = type)) +
  geom_line(size = 1.5) +
  scale_color_manual(name = NULL,
                     values = c("total bases" = "darkred",
                                "open access bases" = "darkblue")) +
  scale_y_continuous(labels = scientific_10 ) +
  labs(x = "Year", y = expression( Terabases~(10^12) ),
       title = "Growth of Sequence Read Archive database") +
  theme_bw() +
  NULL

Plot with log scale

sra %>%
  dplyr::select(date, bases, open_access_bases) %>%
  tidyr::pivot_longer(cols = 2:3, names_to = "type", values_to = "bases") %>%
  dplyr::mutate(type = dplyr::case_when(type == "bases" ~ "total bases",
                                 type == "open_access_bases" ~ "open access bases")) %>%
ggplot(mapping = aes(x = date, y = bases, color = type)) + 
  geom_line(size = 1.5) + 
  scale_color_manual(name = NULL,
                     values = c("total bases" = "darkblue",
                                "open access bases" = "darkred")) +
  scale_y_log10(labels = scientific_10 ) +
  labs(x = "Year", y = "bases" ,
       title = "Growth of Sequence Read Archive database") +
  theme_bw() +
  NULL