In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

knitr::opts_chunk$set(echo = TRUE, fig.width = 7, fig.height = 5, root.dir=here::here())
knitr::opts_knit$set(root.dir=here::here())

You can make awesome hex stickers for your R packages using:

• hexSticker
• ggimage lets you render images as data points.
• ggpattern lets you fill objects with patterns or images.
• magick modify PNGs.

MAGMA.Celltyping

# If you're using R<4.1.1, need this version of rvcheck
# devtools::install_version('rvcheck',version='0.1.8') 
library(hexSticker)
library(dplyr)
library(ggplot2)
library(ggimage)
library(ggpattern)# remotes::install_github("coolbutuseless/ggpattern")

Volcano ggplot

Data from here.

{
  tmp <- file.path("/Desktop/volcano_dat")
  if(!file.exists(tmp)){
    URL <- "https://zenodo.org/record/2529117/files/limma-voom_luminalpregnant-luminallactate?download=1"   
  download.file(URL, tmp)
  } 
  vdat <- data.table::fread(tmp)
}

### Scatter plot data
vdat <- subset(vdat, P.Value < .05 & P.Value >  0.00001 & abs(logFC)< 5 ) 

{
  gg_volcano <- ggplot(vdat, 
         aes(x = logFC * log10(abs(logFC))^3, 
             y = -adj.P.Val,
             color= -adj.P.Val)) +
  geom_point(alpha = .5, show.legend = FALSE,
             aes(size = AveExpr/10)) + 
  geom_point(alpha = 1, shape = 20, show.legend = FALSE, 
             aes(size = AveExpr/100)) + 
  scale_color_gradientn(colours=pals::plasma(100), guide = "colourbar") +
  #### Trapezoid ####
  # geom_polygon(data = trap_dat, aes(x=x, y=y, fill = fill, group = id), inherit.aes = FALSE) 
  theme_void()
print(gg_volcano)
}

ggimage subplot

ggimage

img <- png::readPNG(here::here("inst/hex/volcano_black.png"),
                    native = TRUE)
height <- .4
g <- grid::rasterGrob(img, interpolate=FALSE,
                      width = height/1.25, height = height)
gp <-  gg_volcano + 
  annotation_custom(g, ymax = .1, ymin = bottom*1.35) 
print(gp)

hexSticker

hexSticker

s_size = 1.4
stick <- hexSticker::sticker(subplot = gp, 
                             package="MAGMA.Celltyping", 
                             p_size=14, p_y = 1.45,
                             s_x=1, s_y=.7, s_width = s_size*1.2, s_height = s_size*.9,
        h_fill = "black", h_color = "#C0C0C0",
        spotlight = TRUE, l_alpha = .3,
        filename=here::here("inst/hex/hex.png"), dpi = 300)
print(stick)

Session Info

utils::sessionInfo()

NathanSkene/MAGMA_Celltyping documentation built on May 19, 2024, 7:23 a.m.