Creating a drawProteins hex sticker...

Lots of Bioconductor packages have created hex stickers - those fun stickers that go on the top of your laptop. They are a bit nerdy but, hey, who doesn't like nerdy 😀

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

Some Resources:

• Using drawProteins to draw MAP kinase proteins
• Using drawProteins step by step guide on Bioconductor

For more help, bug reports or to suggest features

• drawProteins on Github