library(dplyr)
library(Logolas)
library(plyr)
library(grid)
library(gridBase)
library(limma)
aRchaic_cluster_beta = function(mat,
K,
type = c("mutation", "mutation-flank", "mutation-pos", "mutation-flank-pos",
"specific-mutation-pos", "wo-strand", "wo-strand-break"),
tol=0.01,
pattern = NULL,
max_pos = 20,
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(),
graph.control = list(),
topics.control = list(),
output_dir = NULL,
structure_width = 5,
structure_height = 8,
inflation = rep(2,1,2),
output_width = 1200,
output_height = 700){
if(type == "mutation"){
aRchaic_cluster_beta_mutation(mat=mat, K=K, tol=tol,
labs = labs, levels = levels, flanking_bases = flanking_bases,
gom_method = gom_method, topic_cols = topic_cols,
structure.control = structure.control,
logo.control = graph.control, topics.control = topics.control,
output_dir = output_dir, structure_width = structure_width,
structure_height = structure_height,
output_width = output_width, output_height = output_height)
}
else if(type == "mutation-flank"){
aRchaic_cluster_beta_mutation_flank(mat=mat, K=K, tol=tol,
labs = labs, levels = levels, flanking_bases = flanking_bases,
gom_method = gom_method, topic_cols = topic_cols,
structure.control = structure.control,
logo.control = graph.control, topics.control = topics.control,
output_dir = output_dir, structure_width = structure_width,
structure_height = structure_height, inflation = inflation,
output_width = output_width, output_height = output_height)
}
else if(type == "mutation-pos"){
aRchaic_cluster_beta_mutation_pos(mat=mat, K=K, tol=tol, max_pos = max_pos,
labs = labs, levels = levels, flanking_bases = flanking_bases,
gom_method = gom_method, topic_cols = topic_cols, structure.control = structure.control,
logo.control = graph.control, topics.control = topics.control,
output_dir = output_dir, structure_width = structure_width,
structure_height = structure_height,
output_width = output_width, output_height = output_height)
}
else if(type == "mutation-flank-pos"){
aRchaic_cluster_beta_mutation_flank_pos(mat=mat, K=K, tol=tol, max_pos = max_pos,
labs = labs, levels = levels, flanking_bases = flanking_bases,
gom_method = gom_method, topic_cols = topic_cols, structure.control = structure.control,
logo.control = graph.control, topics.control = topics.control,
output_dir = output_dir, structure_width = structure_width,
structure_height = structure_height, inflation = inflation,
output_width = output_width, output_height = output_height)
}
else if(type == "specific-mutation-pos"){
if(is.null(pattern)){
stop("for this option, user needs to provide a mutation type: C->T, C->A C->G, T->A, T->C or T->G")
}
aRchaic_cluster_beta_pos(mat=mat, pattern = pattern, K=K, tol=tol, max_pos = max_pos,
labs = labs, levels = levels, flanking_bases = flanking_bases,
gom_method = gom_method, topic_cols = topic_cols,
structure.control = structure.control,
graph.control = graph.control,
topics.control = topics.control,
output_dir = output_dir, structure_width = structure_width,
structure_height = structure_height,
output_width = output_width, output_height = output_height)
}
else if(type == "wo-strand"){
aRchaic_cluster_beta_wo_strand(mat=mat, K=K, tol=tol, max_pos = max_pos,
labs = labs, levels = levels, flanking_bases = flanking_bases,
gom_method = gom_method, topic_cols = topic_cols, structure.control = structure.control,
logo.control = graph.control, topics.control = topics.control,
output_dir = output_dir, structure_width = structure_width,
tructure_height = structure_height, inflation = inflation,
output_width = output_width, output_height = output_height)
}
else if(type == "wo-strand-break"){
aRchaic_cluster_beta_wo_strand_break(mat=mat, K=K, tol=tol, max_pos = max_pos,
labs = labs, levels = levels, flanking_bases = flanking_bases,
gom_method = gom_method, topic_cols = topic_cols, structure.control = structure.control,
logo.control = graph.control, topics.control = topics.control,
output_dir = output_dir, structure_width = structure_width,
tructure_height = structure_height, inflation = inflation,
output_width = output_width, output_height = output_height)
}else{
stop("the type of filtering does not match with the possible options: see documentation")
}
}
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