## ----load_packages, eval = TRUE, echo=FALSE----------------------------------- library(BiocStyle) library(drawProteins) library(ggplot2) library(knitr) opts_chunk$set(comment=NA, fig.align = "center", out.width = "100%", dpi = 100) ## ----load_NFkappaB_data, fig.height=10, fig.wide = TRUE----------------------- # load up data for five NF-kappaB proteins data("five_rel_data") max(five_rel_data$order) # returns 5 # use extract_transcripts() to create a new data frame prot_data <- extract_transcripts(five_rel_data) max(prot_data$order) # returns 7 ## ----check_chains, fig.height=10, fig.wide = TRUE----------------------------- p1 <- draw_canvas(five_rel_data) p1 <- draw_chains(p1, five_rel_data) p1 <- p1 + ggtitle("Five chains plotted") p2 <- draw_canvas(prot_data) p2 <- draw_chains(p2, prot_data) p2 <- p2 + ggtitle("Seven chains plotted") p1 p2 ## ----draw_domains_and_phospho, fig.height=10, fig.wide = TRUE----------------- p2 <- draw_domains(p2, prot_data) p2 <- draw_phospho(p2, prot_data, size =8) p2 ## ----draw_canvas_and_chains, fig.height=8, fig.wide = TRUE-------------------- p2 <- draw_canvas(prot_data) p2 <- draw_chains(p2, prot_data, fill = "lightsteelblue1", outline = "grey", labels = c("p105", "p105", "p100", "p100", "Rel B", "c-Rel", "p65/Rel A", "p50", "p52"), label_size = 5) p2 <- draw_phospho(p2, prot_data, size = 8, fill = "red") p2 + theme_bw() ## ----session_Info, echo=FALSE------------------------------------------------- sessionInfo()