#' plot_sim
#'
#' generate visualizations for rlda object
#'
#' @include rlda_c.R
#' @param r a rlda object
#' @param dir directory to save generated plots (no "/" at the end)
#' @exportMethod plot_sim
#'
setGeneric("plot_sim", function(r, dir)standardGeneric("plot_sim"))
setMethod("plot_sim",
signature(r = "rlda", dir = "character"),
function (r, dir) {
k = r@K
dir.create(paste0(dir,"/sim"))
# plot similarity matrix
similarity_list_mat = do.call(cbind, r@similarity_mat_list)
mod_idx = rep(1:length(k), k)
#idx_mat = cbind(mod_idx, unlist(lapply(k, function(x) 1:x)))
#colnames(similarity_list_mat) = paste(1:dim(similarity_list_mat)[2])
#rownames(similarity_list_mat) = paste(1:dim(similarity_list_mat)[1])
#colnames(similarity_list_mat) = paste('t[',1:dim(similarity_list_mat)[2],']',sep='')
#colnames(similarity_list_mat) = paste('t[',idx_mat[,1],idx_mat[,2],']',sep='')
#rownames(similarity_list_mat) = paste('t[',1:dim(similarity_list_mat)[1],']',sep='')
#sim_melt = melt(similarity_list_mat)
#sim_melt$mod_i = paste('m[',rep(1:length(k), k*44),']',sep=)
#x_tick_lab = parse(text = levels(as.factor(sim_melt$Var2)))
#y_tick_lab = parse(text = levels(as.factor(sim_melt$Var1)))
for (i in 1:length(r@similarity_mat_list)){
similarity_list_mat = r@similarity_mat_list[[i]]
#colnames(similarity_list_mat) = paste(1:dim(similarity_list_mat)[2])
#rownames(similarity_list_mat) = paste(1:dim(similarity_list_mat)[1])
#colnames(similarity_list_mat) = paste('t[',1:dim(similarity_list_mat)[2],']',sep='')
colnames(similarity_list_mat) = paste('t[',i,'*","*',1:dim(similarity_list_mat)[2],']',sep='')
rownames(similarity_list_mat) = paste('t[',1:dim(similarity_list_mat)[1],']',sep='')
sim_melt = melt(similarity_list_mat)
#sim_melt$mod_i = rep(1:length(r@K), r@K*10)
x_tick_lab = parse(text = levels(as.factor(sim_melt$Var2)))
y_tick_lab = parse(text = levels(as.factor(sim_melt$Var1)))
myplot<-ggplot(sim_melt, aes(x=as.numeric(as.factor(Var2)), y=as.numeric(as.factor(Var1))))+
geom_tile(aes(fill=value), color='white')+
geom_text(aes(label=round(value, 2)), color='beige', size=2.5)+
ggtitle("topic similarities")+
#scale_fill_gradient2(low="white", high="black", midpoint = 0.1)+
scale_fill_continuous(low="#56B1F7", high="#132B43", guide = guide_legend(title = "similarity"))+
scale_x_continuous(breaks=1:length(x_tick_lab),labels = rev(x_tick_lab), expand = c(0,0))+
scale_y_continuous(breaks = 1:length(y_tick_lab),
labels = y_tick_lab,
sec.axis = dup_axis(),
expand = c(0,0))+
xlab("Comparison Model Topics\n")+
ylab("\nOriginal Model Topics\n")+
#facet_grid(rev(mod_i)~., scales = "free", space = "free")+
coord_flip()+
theme(panel.background = element_rect("white"),
legend.position="bottom",
axis.text = element_text(size = 14))
ggsave(paste0("sim", i, ".jpg"), plot=myplot,
path = paste0(dir,"/sim"),
width = 12, height = 12)
}
})
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