I thought I should create a hex sticker for drawProteins since it's now available in Bioconductor.
It's been created totally in R using the hexSticker package from the talented GuangchuangYu.
Here is the sticker:
Below is the R code that makes the sticker. I've chosen to show three of NF-kappaB proteins but the code could be adapted to illustrate your favourite protein. You can also customise the sticker colour and lots of other things.
START
# script to create drawProteins sticker
# setwd("/Users/paulbrennan/Documents/drawProteins_hexsticker")
library(ggplot2)
# install.packages("hexSticker")
library(hexSticker)
library(drawProteins)
data("five_rel_data")
p <- draw_canvas(five_rel_data)
p <- draw_chains(p, five_rel_data, label_chains = FALSE, size =0.2)
p <- draw_domains(p, five_rel_data,
show.legend = FALSE,
label_size = 2)
p
p <- draw_phospho(p, five_rel_data)
p <- p + theme_void()
sticker(p, package="drawProteins", p_size=6, s_x=.98,
s_y=.88, s_width=1.4, s_height=1.1,h_fill = "#114466", h_color="#001030")
# this doesn't quite work :-(
# size of text is wrong... no labels... cramped!
# I think five proteins is probably too many...
# reduce to three....
# P19838
# Q04206
# Q04864
# get from UniProt rather than using internal data
prot_data <- drawProteins::get_features("Q04206 Q04864 P19838")
# turn the data into a dataframe
prot_data <- drawProteins::feature_to_dataframe(prot_data)
# create canvas
p <- draw_canvas(prot_data)
# customise the labels
p <- draw_chains(p, prot_data, label_size = 1.4,
labels = c("c-Rel",
"p50/p105",
"p50/p105",
"p65/Rel A"),
size=0.2)
# draw domains without a legend or labels
p <- draw_domains(p, prot_data, show.legend = FALSE, label_domains = FALSE)
# add text and control size with geom_text rather than labels from drawProteins
p <- p + ggplot2::geom_text(data = prot_data[prot_data$type == "DOMAIN", ],
ggplot2::aes(x = begin + (end-begin)/2,
y = order,
label = description),
size = 1.3)
# keep phosphorylation sites small
p <- draw_phospho(p, prot_data, size = 1)
# a completely blank theme using theme_void()
p <- p + theme_void()
p
# make the sticker using the ggplot object entitled p
# creates a png file
sticker(p,
package="drawProteins",
p_size=6, # font size for package name
s_x=.95, # x position for ggplot object
s_y=.86, # y position for ggplot object
s_width=1.4,
s_height=1.1,
h_fill = "#e8a935", # background colour for hexagon
h_color="#001030", # border colour
url = "www.bioconductor.org")
# automatically creates the PNG file with the name drawProteins.
# make the PDF
sticker(p,
package="drawProteins",
p_size=6, # font size for package name
s_x=.95, # x position for ggplot object
s_y=.86, # y position for ggplot object
s_width=1.4,
s_height=1.1,
h_fill = "#e8a935", # background colour for hexagon
h_color="#001030", # border colour
url = "www.bioconductor.org",
filename="drawProteins.pdf")
END
