scdb: automates fetching of Valentine Svenssen's single-cell...

In trichelab/velocessor: The world's dumbest single-cell RNA velocity calculator and loader

Description

scdb() tidies up the database a bit, with Date, URL, Cells, and Velocity

Usage

scdb(URL = "http://www.nxn.se/single-cell-studies/data.tsv", ...)

Arguments

URL	the URL if it changes
...	anything else to tell utils::read.delim

Details

The database itself lives at http://www.nxn.se/single-cell-studies/data.tsv

Value

 a data.frame, with the Date column as an actual Date

References

Svensson V, Beltrame EdV, Pachter L (2020), A curated database reveals trends in single-cell transcriptomics, Database, 28 November 2020 https://doi.org/10.1093/database/baaa073

Examples

  db <- scdb()

  library(useful)
  library(tidyverse)
  subset(db, Velocity == TRUE) %>% corner

  columns <- c("Title", "Data.location", "URL")
  subset(db, Tissue == "Blood" & Cells > 50000)[, columns]
  subset(db, grepl("CITE", Technique))[, columns]
  subset(db, grepl("Amit", Authors))[, columns]

  a_year_ago <- (Sys.Date() - 365)
  subset(db, Date > a_year_ago) %>% corner

  five_years_ago <- (Sys.Date() - (5*365.25))
  p1 <- ggplot(subset(db, Date > five_years_ago), 
               aes(x = Date, fill = Velocity)) + 
    geom_histogram() + 
    scale_x_date() + 
    xlab("year") + 
    scale_y_log10() + 
    ylab("papers") + 
    NULL 

  suppressWarnings(p1 + theme_minimal() + ggtitle("Velocity in papers"))

  p2 <- ggplot(subset(db, 
                      Organism %in% c("Human", "Mouse", "Zebrafish") & 
                      Date > five_years_ago), 
               aes(x=Date, y=Cells, color=Organism, fill=Organism)) + 
    geom_point() + 
    geom_smooth() + 
    scale_y_log10() + 
    NULL

  suppressWarnings(p2 + facet_grid(vars(Organism)) + theme_minimal())

trichelab/velocessor documentation built on Jan. 5, 2022, 6:27 p.m.