Nothing
suppressMessages(library(dplyr))
suppressMessages(library(tibble))
load(system.file("testdata", "DBS.rda", package="tableExtra"))
load(system.file("testdata", "DEXP.rda", package="tableExtra"))
load(system.file("testdata", "pcawg_counts.rda", package="tableExtra"))
load(system.file("testdata", "sbs_aetiologies.rda", package="tableExtra"))
cat(paste("tempdir located at", tempdir(), "\n"))
plot_grob <- function(g, name, width=NULL, height=NULL){
grDevices::pdf(file=file.path(tempdir(), name),
width=width,
height=height,
onefile=T)
grid::grid.draw(g)
grDevices::dev.off()
invisible(list(plot_success=T))
}
pcawg_plot_data <- function(){
scale_breaks <- seq(from=0, to=1, by=0.1)
color_palette <- c("#ffc651", "#ffa759", "#ff8962", "#ff6b6b", "#cc6999", "#9968c8", "#6767f8", "#4459ce", "#224ba5",
"#013d7c")
color_breaks <- c(0, 0.05, 0.1, 0.25, 0.5, 1, 2.5, 5, 10, 25, 1e6)
color_bg <- c("#f8f9fa", "#e9ecef")
theme <- ttheme_awesome(base_size=12,
rep_mode="col",
core_size=5,
scale_breaks=scale_breaks,
color_palette=color_palette,
color_breaks=color_breaks,
core=list(bg_params=list(fill=color_bg)))
# define dscale and cols_more from PCAWG data
dscale <- pcawg_counts %>%
dplyr::group_by(Cancer.Types) %>%
dplyr::mutate(n=dplyr::n()) %>%
dplyr::summarize_at(dplyr::vars(-Sample.Names, -Accuracy), ~sum(.x>0)) %>%
dplyr::mutate_at(dplyr::vars(-Cancer.Types,-n), ~./n)
cols_more <- list("n="=dscale$n)
dscale$n <- NULL
dscale <- tibble::column_to_rownames(.data=dscale, var="Cancer.Types")
dscale <- t(as.matrix(dscale))
# define dcolor and rows_more from PCAWG data
rows_more <- list("Aetiology"=sbs_aetiologies[sbs_aetiologies$Signature %in% rownames(dscale), "Aetiology"])
dcolor <- pcawg_counts %>%
dplyr::group_by(Cancer.Types) %>%
dplyr::summarize_at(dplyr::vars(-Sample.Names, -Accuracy), ~median(.[.!=0]*1e6/3.2e9)) %>%
replace(is.na(.),0)
dcolor <- tibble::column_to_rownames(.data=dcolor, var="Cancer.Types")
dcolor <- t(as.matrix(dcolor))
list(dscale=dscale, dcolor=dcolor, cols_more=cols_more, rows_more=rows_more, theme=theme)
}
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