############# aRchaic_cluster_beta_1 () ############################
aRchaic_cluster_beta_mutation = function(mat,
K,
tol=0.01,
labs = NULL,
levels = NULL,
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(),
logo.control = list(),
topics.control = list(),
output_dir = NULL,
structure_width = 5,
structure_height = 8,
output_width = 1200,
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)
logo.control.default <- list(ic = NULL, hist = TRUE, frame_width =1,
ic.scale = FALSE,
xaxis_fontsize = 10, xlab_fontsize = 15,
y_fontsize = 15, main_fontsize = 16, start = 0.001,
yscale_change = TRUE, pop_name = paste0("logo plot mutation"), xlab = "",
ylab = "composition", col_line_split = "grey80", scale0 = 0.01,
scale1 = 0.99, newpage = TRUE)
structure.control <- modifyList(structure.control.default, structure.control)
logo.control <- modifyList(logo.control.default, logo.control)
topics.control <- modifyList(topics.control.default, topics.control)
mat_reduced <- filter_by_mutation(mat)
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$theta
signature_set <- rownames(theta_pool)
theta <- dplyr::tbl_df(data.frame(theta_pool)) %>% dplyr::mutate(sig = signature_set) %>% dplyr::group_by(sig) %>% dplyr::summarise_each(funs(sum)) %>% as.data.frame()
rownames(theta) <- theta[,1]
theta <- theta[,-1]
mutations <- as.character(sapply(rownames(theta), function(x) return(paste0(strsplit(x,"")[[1]][-2], collapse = ""))))
rownames(theta) <- mutations
for(m in 1:dim(theta)[2]){
tab <- matrix(theta[,m], nrow=length(theta[,1]))
rownames(tab) <- rownames(theta)
colnames(tab) <- "mutation"
cols = RColorBrewer::brewer.pal.info[RColorBrewer::brewer.pal.info$category == 'qual',]
col_vector = unlist(mapply(RColorBrewer::brewer.pal, cols$maxcolors, rownames(cols)))
total_chars = c("A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O",
"P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z", "zero", "one", "two",
"three", "four", "five", "six", "seven", "eight", "nine", "dot", "comma",
"dash", "colon", "semicolon", "leftarrow", "rightarrow")
cols = RColorBrewer::brewer.pal.info[RColorBrewer::brewer.pal.info$category == 'qual',]
col_vector = unlist(mapply(RColorBrewer::brewer.pal, cols$maxcolors, rownames(cols)))
color_code = sample(col_vector, length(total_chars), replace=FALSE)
color_code[c(1,3,7,20, 43)] <- c("green", "blue", "orange", "red", "gray")
color_profile <- list("type" = "per_symbol",
"col" = color_code)
plot.new()
png(paste0(output_dir, "logo_clus_", m, ".png"), width=output_width, height = output_height)
do.call(Logolas::logomaker, c(list(table=tab, color_profile = color_profile),
logo.control))
dev.off()
}
graphics.off()
message("Finished")
}
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