############# aRchaic_cluster_beta_pos () ############################
aRchaic_cluster_beta_pos = function(mat,
pattern = "C->T",
K,
tol=0.01,
labs = NULL,
levels = NULL,
max_pos = 20,
flanking_bases = 1,
gom_method = "independent",
topic_cols = c("red","blue","darkgoldenrod1","cyan","firebrick", "green",
"hotpink","burlywood","yellow","darkgray","deepskyblue","darkkhaki",
"brown4","darkorchid","magenta","yellow", "azure1","azure4"),
structure.control = list(),
graph.control = list(),
topics.control = list(),
output_dir = NULL,
structure_width = 5,
structure_height = 8,
output_width = 500,
output_height = 700){
if(is.null(output_dir)){
output_dir <- paste0(getwd(), "/")
}
topics.control.default <- list(bf = FALSE, kill = 2, ord = TRUE, verb = 1, admix = TRUE,
nbundles = 1, use_squarem = FALSE, init.adapt = FALSE, type = "full",
light = 1, method_admix = 1, sample_init = TRUE, tmax = 10000)
structure.control.default <- list(yaxis_label = "aRchaic pops",
order_sample = FALSE,
figure_title = paste0(" StructurePlot: K=", K,""),
axis_tick = list(axis_ticks_length = .1,
axis_ticks_lwd_y = .1,
axis_ticks_lwd_x = .1,
axis_label_size = 10,
axis_label_face = "bold"),
legend_title_size = 10,
legend_key_size = 0.7,
legend_text_size = 8)
graph.control.default <- list(col="red",
cex=unit(1, "npc"), pch=unit(16,"npc"),
xlab="position", ylab="prob. of mutation",
main=paste0("mutation trend:", pattern),
cex.axis=unit(1, "npc"),
cex.main=unit(1, "npc"))
structure.control <- modifyList(structure.control.default, structure.control)
graph.control <- modifyList(graph.control.default, graph.control)
topics.control <- modifyList(topics.control.default, topics.control)
mat_reduced <- filter_by_pos_pattern(mat, max_pos = max_pos,
pattern = pattern)
signature_set <- colnames(mat_reduced)
if(gom_method == "full"){
message("Fitting the Grade of Membership Model - full version - due to Matt Taddy")
suppressWarnings(topic_clus <- do.call(maptpx::topics, append(list(counts = mat_reduced, K=K, tol=tol, model = "full", signatures = NULL), topics.control)))
save(topic_clus, file = paste0(output_dir, "model.rda"))
}
if(gom_method == "independent"){
message("Fitting the Grade of Membership Model - full version - due to Y. Shiraichi and M. Stephens")
suppressWarnings(topic_clus <- do.call(maptpx::topics, append(list(counts = mat_reduced, K=K, tol=tol, model = "independent", signatures = signature_set), topics.control)))
save(topic_clus, file = paste0(output_dir, "model.rda"))
}
if(is.null(labs)){
labs <- rownames(mat_reduced)
}
if(is.null(levels)){
levels <- unique(labs)
}
message ("Structure plot and Logo plot representations of clusters")
if(is.null(output_dir)){ output_dir <- paste0(getwd(),"/")}
omega <- topic_clus$omega
annotation <- data.frame(
sample_id = paste0("X", c(1:NROW(omega))),
tissue_label = factor(labs, levels = levels)
)
rownames(omega) <- annotation$sample_id
plot.new()
grid.newpage()
do.call(StructureGGplot, append(list(omega= omega,
annotation = annotation,
palette = topic_cols),
structure.control))
ggplot2::ggsave(paste0(output_dir, "structure.png"), width = structure_width,
height = structure_height)
theta_pool <- topic_clus$theta
pos <- sapply(rownames(theta_pool), function(x) return(strsplit(x, "_")[[1]][2]))
rownames(theta_pool) <- pos
max_prob <- max(theta_pool)
theta_pool_mod <- theta_pool[match(1:max_pos, as.numeric(rownames(theta_pool))),]
plot(1, type="n", axes=F, xlab="", ylab="")
for(l in 1:dim(theta_pool_mod)[2]){
png(paste0(output_dir, "plot_clus_", l, ".png"), width=output_width, height = output_height)
do.call(plot_graph_2, c(list(probs = theta_pool_mod[,l],
max_pos = max_pos,
max_prob = max_prob),
graph.control))
dev.off()
}
graphics.off()
message("Finished")
}
plot_graph_2 <- function(probs, max_pos, max_prob, col="red",
cex=unit(1, "npc"), pch=unit(16,"npc"),
xlab="position", ylab="prob. of mutation",
main="",
cex.axis=unit(1, "npc"),
cex.main=unit(1, "npc")){
# if (length(probs) != max_pos){
# stop(cat('probability vector must be of length ', max_pos))
# }
par(font.axis = 2)
plot(as.numeric(names(probs)), probs/max_prob, xlim = c(0, max_pos), ylim=c(0,1),
type = "b", xaxt = "n", yaxt = "n", cex = cex, pch=pch, col=col, main=main,
cex.main=cex.main, ylab="", xlab="")
axis(side = 1, at = floor(seq(1, max_pos, length.out=5)), cex.axis = cex.axis, lwd.ticks = 1, tck=-0.05,
cex.lab=2, mgp=c(2.5, 0.5, 0))
title(xlab = xlab, mgp=c(2.5,1.5,0), cex.lab=1.8)
ylimit <- c(0.0, 0.5, 1.0)*max_prob
axis(side = 2, at = c(0.0, 0.5, 1.0), labels = round(ylimit,2), cex.axis = cex.axis, lwd.ticks=1, tck=-0.05,
cex.lab=2, mgp=c(2.5, 0.5, 0))
title(ylab = ylab, mgp=c(2.5,1,0), cex.lab=1.8)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.