library(rmongodb)
library(stringr)
library(ggplot2)
library(knitr)
library(gridExtra)
library(reshape)
library(igraph)

mongo <- mongo.create()
if(mongo.is.connected(mongo) == TRUE) {
    db <- mongo.get.databases(mongo)
    coll <- mongo.get.database.collections(mongo, db)
}

df <- data.frame(names = mongo.distinct(mongo, coll, 'from'))
df$isProf <- str_detect(toupper(df$names), "PROFESSOR")
ggplot(df, aes(x = factor(1), fill = isProf) ) + geom_bar()  + coord_polar(theta = "y")+ theme(axis.title.x=element_blank(),        
        axis.text.x=element_blank(),
        axis.title.y=element_blank(),
        axis.text.y=element_blank())

## [1] "JOURNAL ARTICLE"  "CONFERENCE PAPER" "BOOK CHAPTER"    
## [4] "PATENT"           "REPORT"           "SOFTWARE"        
## [7] "OTHER"            "BOOK"             "POSTER"

df <- mongo.find.all(mongo, coll, fields = list('publication-type' = 1, '_id' = 0), data.frame = T)
ggplot(df, aes(x = publication.type) ) + geom_bar() +  geom_text(aes(label = ..count..), stat = "count", vjust = -1)+ theme(axis.text.x = element_text(angle = 90, hjust = 1)) + scale_y_log10(breaks = c(1,10,100,1000,10000))

main <- mongo.find.all(mongo, coll, query=list("$or" = list(list("publication-type" = "JOURNAL ARTICLE"), list("publication-type" = "CONFERENCE PAPER"))), fields = list('publication-type' = 1, 'title' = 1, 'num_citations' = 1, 'journal' = 1, 'year' = 1, 'from' = 1, '_id' = 0))


#  Only keeps data entries that have all the header fields defined.
list2df <- function(list, headers){
    output = list()
    for(i in 1:length(list)){
        record = T
        for(j in headers){
            if(is.null(list[[i]][[j]])){
                record = F
                break
            }
        }
        if(record == T){
            for(j in headers)
                output[[j]] <-  c(output[[j]], list[[i]][[j]])
        }
    }
    return(as.data.frame(output))
}

df <- list2df(main, c('journal', 'title'))

df <- df[!duplicated(df$title), ]
ggplot(df, aes(x = journal) ) + geom_bar() + theme(axis.text.x=element_blank(),axis.ticks=element_blank())

q <- aggregate(df$journal, by=list(df$journal), length)
colnames(q) <- c("Journal.Names", "Submission")
q <- q[order(q$Submission, decreasing = T),]
kable(tail(q, 10), row.names = F)

kable(head(q, 10), row.names = F)

q$Journal.Names <- factor(q$Journal.Names, levels = q$Journal.Names)
ggplot(q[1:20, ], aes(x = Journal.Names, y = Submission)) + geom_bar(stat = "identity") + theme(axis.text.x = element_text(angle = 90, hjust = 1))

df <- list2df(main, c('title', 'num_citations'))
df$title <- str_trim(df$title)
df <- df[!duplicated(df$title), ]
df <- df[order(df$num_citations, decreasing = T), ]
ggplot(df, aes(x = num_citations)) + geom_bar() + xlim(0, 250) + ylim(0,300)

df <- list2df(main, c('title', 'year', 'num_citations', 'from'))
ggplot(df, aes(year, num_citations)) + geom_point() + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + ylim(0, 2500)

df$isProf <- str_detect(toupper(df$from), "PROFESSOR")
ggplot(data = df, mapping = aes(x = num_citations)) + facet_grid(isProf~., scale = 'free') + geom_histogram(data = subset(df, isProf == F), binwidth = 1, fill = "red", alpha = 0.5) + geom_histogram(data = subset(df, isProf == T), binwidth = 1 , fill = "blue", alpha = 0.5) + xlim(0, 250) + ylim(0, 300)

q <- aggregate(df$from, by = list(df$from), length)
colnames(q) <- c('name', 'num_publications')
q$isProf <- str_detect(toupper(q$name), "PROFESSOR")
ggplot(data = q, mapping = aes(x = num_publications)) + facet_grid(isProf~., scale = 'free') + geom_histogram(data = subset(q, isProf == F), fill = "red", alpha = 0.5) + geom_histogram(data = subset(q, isProf == T), fill = "blue", alpha = 0.5) + ylab("Number of Profs / Docs")

df <- list2df(main, c('from', 'title'))
df$title <- iconv(df$title,"WINDOWS-1252","UTF-8")
df$title <- toupper(df$title)
q <- unique(df$title)
q <-sapply(q, function(i){
    length(unique(df$from[df$title == i]))
})
p <- names(q[q > 1])
s <- unique(df$from[df$title %in% p])

heatmap <- function(matrix, xlabel = NULL, ylabel = NULL, fill = NULL, color= NULL, text_size = 7){
    matrix <- as.data.frame(matrix)
    colors <- c("steelblue", "seagreen", "darkorchid", "maroon")
    melt <- melt(matrix)
    if(ncol(melt) == 2){
        melt$variable1 <- melt$variable
        melt$variable2 <- rep(rownames(matrix), nrow(matrix))
        melt$variable1 <- factor(melt$variable1, levels = (unique(as.character(rownames(matrix)))))
        melt$variable2 <- factor(melt$variable2, levels = rev(unique(as.character(rownames(matrix)))))
    }
    p <- ggplot(melt,aes(x = variable1, y = variable2)) + geom_tile(aes(fill = value), colour = "white") + scale_fill_gradient(high = "white", low = "black")
    p <- p + geom_text(aes(fill = value, label = round(value,2)), size = text_size) + labs(x = xlabel, y = ylabel, fill = fill) + theme(axis.text.x = element_text(angle = 90)) + theme(legend.position = "none")
}

staffs <- as.character(sort(s))
matrix <- matrix(0, nrow = length(staffs), ncol = length(staffs))
colnames(matrix) <- rownames(matrix) <- staffs
collaborations <- lapply(p,function(i) df$from[(df$title == i)] )
for(i in collaborations){
    for(j in 1:(length(i) - 1)){
        for(k in (j + 1):length(i)){
            r <- which(i[j] == staffs)
            c <- which(i[k] == staffs)
            if(r != c)
                matrix[r, c] <- matrix[c, r] <- 1 + matrix[r, c]
        }
    }
}    
#diag(matrix) <- 0
diagnol <- data.frame(x1 = 100, y1 = 1, x2 = 1, y2 = 100)
colnames(matrix) <- rownames(matrix) <- 1:length(staffs)
p <- heatmap(matrix, text_size = 3)
p + geom_segment(data = diagnol, aes(x = x1, y = y1, xend = x2, yend = y2, colour = "white"))

kable(data.frame(Name = staffs, Index = (1:length(staffs))), row.names = F)

ggplot(data.frame(x = sapply(collaborations, function(i) length(i))), aes(x) ) + geom_bar() +  geom_text(aes(y = ..count.. , label = ..count..), stat = "count", vjust = -1) + scale_y_log10() + scale_x_discrete() + xlab("Number of staffs contributed to the paper")

adjMat <- matrix > 0
net <- graph_from_adjacency_matrix(adjMat)
plot(net, edge.arrow.size = 0,  vertex.size = 5, vertex.label.cex = 0.5)