# The packages can be installed within R with:
# intstall.packages(c("tidyverse", "ggrepel"))

# Load packages
library(tidyverse)
library(ggrepel)

# A short function for outputting the tables
knitr_table <- function(x) {
  x %>% 
    knitr::kable(format = "html", digits = Inf, 
                 format.args = list(big.mark = ",")) %>%
    kableExtra::kable_styling(font_size = 15)
}


# Import data
data <- read_tsv("https://raw.githubusercontent.com/sdgamboa/misc_datasets/master/L0_vs_L20.tsv")
dim(data)

## [1] 20945     4

head(data) %>% 
 knitr_table()

p1 <- ggplot(data, aes(logFC, -log(FDR,10))) + # -log10 conversion  
  geom_point(size = 2/5) +
  xlab(expression("log"[2]*"FC")) + 
  ylab(expression("-log"[10]*"FDR"))
p1

data <- data %>% 
  mutate(
    Expression = case_when(logFC >= log(2) & FDR <= 0.05 ~ "Up-regulated",
                           logFC <= -log(2) & FDR <= 0.05 ~ "Down-regulated",
                           TRUE ~ "Unchanged")
    )
head(data) %>% 
  knitr_table()

p2 <- ggplot(data, aes(logFC, -log(FDR,10))) +
  geom_point(aes(color = Expression), size = 2/5) +
  xlab(expression("log"[2]*"FC")) + 
  ylab(expression("-log"[10]*"FDR")) +
  scale_color_manual(values = c("dodgerblue3", "gray50", "firebrick3")) +
  guides(colour = guide_legend(override.aes = list(size=1.5))) 
p2

data %>% 
  count(Expression) %>% 
  knitr_table()

data <- data %>% 
  mutate(
    Significance = case_when(
      abs(logFC) >= log(2) & FDR <= 0.05 & FDR > 0.01 ~ "FDR 0.05", 
      abs(logFC) >= log(2) & FDR <= 0.01 & FDR > 0.001 ~ "FDR 0.01",
      abs(logFC) >= log(2) & FDR <= 0.001 ~ "FDR 0.001", 
      TRUE ~ "Unchanged")
  )
head(data) %>% 
  knitr_table()

p3 <- ggplot(data, aes(logFC, -log(FDR,10))) +
  geom_point(aes(color = Significance), size = 2/5) +
  xlab(expression("log"[2]*"FC")) + 
  ylab(expression("-log"[10]*"FDR")) +
  scale_color_viridis_d() +
  guides(colour = guide_legend(override.aes = list(size=1.5))) 

p3

data %>% 
  count(Expression, Significance) %>% 
  knitr_table()

top <- 10
top_genes <- bind_rows(
  data %>% 
    filter(Expression == 'Up-regulated') %>% 
    arrange(FDR, desc(abs(logFC))) %>% 
    head(top),
  data %>% 
    filter(Expression == 'Down-regulated') %>% 
    arrange(FDR, desc(abs(logFC))) %>% 
    head(top)
)
top_genes %>% 
  knitr_table()

p3 <-  p3 +
  geom_label_repel(data = top_genes,
                   mapping = aes(logFC, -log(FDR,10), label = Genes),
                   size = 2)
p3

info <- sessionInfo()
toLatex(info, locale = FALSE)

## \begin{itemize}\raggedright
##   \item R version 4.0.3 (2020-10-10), \verb|x86_64-pc-linux-gnu|
##   \item Running under: \verb|Ubuntu 20.04.1 LTS|
##   \item Matrix products: default
##   \item BLAS:   \verb|/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0|
##   \item LAPACK: \verb|/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0|
##   \item Base packages: base, datasets, graphics, grDevices, methods,
##     stats, utils
##   \item Other packages: dplyr~1.0.2, forcats~0.5.0, ggplot2~3.3.2,
##     ggrepel~0.8.2, purrr~0.3.4, readr~1.3.1, stringr~1.4.0,
##     tibble~3.0.3, tidyr~1.1.2, tidyverse~1.3.0
##   \item Loaded via a namespace (and not attached): assertthat~0.2.1,
##     backports~1.1.9, blob~1.2.1, blogdown~0.20, bookdown~0.20,
##     broom~0.7.0, cellranger~1.1.0, cli~2.0.2, colorspace~1.4-1,
##     compiler~4.0.3, crayon~1.3.4, curl~4.3, DBI~1.1.0, dbplyr~1.4.4,
##     digest~0.6.25, ellipsis~0.3.1, evaluate~0.14, fansi~0.4.1,
##     farver~2.0.3, fs~1.5.0, generics~0.0.2, glue~1.4.2, grid~4.0.3,
##     gtable~0.3.0, haven~2.3.1, highr~0.8, hms~0.5.3, htmltools~0.5.0,
##     httr~1.4.2, jsonlite~1.7.1, kableExtra~1.2.1, knitr~1.29,
##     labeling~0.3, lifecycle~0.2.0, lubridate~1.7.9, magrittr~1.5,
##     modelr~0.1.8, munsell~0.5.0, pillar~1.4.6, pkgconfig~2.0.3,
##     R6~2.4.1, Rcpp~1.0.5, readxl~1.3.1, reprex~0.3.0, rlang~0.4.7,
##     rmarkdown~2.3, rstudioapi~0.11, rvest~0.3.6, scales~1.1.1,
##     stringi~1.4.6, tidyselect~1.1.0, tools~4.0.3, vctrs~0.3.4,
##     viridisLite~0.3.0, webshot~0.5.2, withr~2.2.0, xfun~0.16,
##     xml2~1.3.2, yaml~2.2.1
## \end{itemize}