calculate_csi

library(tidyverse)
calculate_csi <- function(regulonAUC,
                          calc_extended = FALSE,
                          verbose = FALSE) {

    compare_pcc <- function(vector_of_pcc, pcc) {
        if (vector_of_pcc>=pcc) {
            return(1)
        } else {
            return(0)
        }
    }

    calc_csi <- function(reg, reg2, pearson_cor) {
        test_cor <- pearson_cor[reg, reg2]-0.05
        total_n <- ncol(pearson_cor)
        pearson_cor_sub1 <- subset(pearson_cor, rownames(pearson_cor) == reg)
        pearson_cor_sub2 <- subset(pearson_cor,rownames(pearson_cor) == reg2 )
        sum1 <- apply(pearson_cor_sub1, MARGIN = 2, FUN = compare_pcc, pcc = test_cor)
        sum2 <- apply(pearson_cor_sub2, MARGIN = 2, FUN = compare_pcc, pcc = test_cor)
        union <- c(names(sum1[sum1 == 1]), names(sum2[sum2 == 1]))
       fraction_lower = 1 - (length(unique(union)) / total_n)
        return(fraction_lower)
    }

    regulonAUC_sub <- regulonAUC@assays@data@listData$AUC

    if (calc_extended == TRUE) {
        regulonAUC_sub <- subset(regulonAUC_sub, grepl("extended", rownames(regulonAUC_sub)))
    } else if (calc_extended == FALSE) {
        regulonAUC_sub <- subset(regulonAUC_sub, !grepl("extended", rownames(regulonAUC_sub)))
    }
    
    regulonAUC_sub <- t(regulonAUC_sub)
    pearson_cor <- cor(regulonAUC_sub)
    pearson_cor_df <- as.data.frame(pearson_cor)
    pearson_cor_df$regulon_1 <- rownames(pearson_cor_df)
    pearson_cor_long <- pearson_cor_df %>%
        gather(regulon_2, pcc, -regulon_1) %>%
        mutate("regulon_pair" = paste(regulon_1, regulon_2, sep = "_"))

    regulon_names <- unique(colnames(pearson_cor))
    num_of_calculations <- length(regulon_names) * length(regulon_names)
    csi_regulons <- data.frame(matrix(nrow = num_of_calculations, ncol = 3))
    colnames(csi_regulons) <- c(
        "regulon_1",
        "regulon_2",
        "CSI"
    )

    num_regulons <- length(regulon_names)

    f <- 0
    for (reg in regulon_names) {
        ## Check if user wants to print info
        if (verbose == TRUE) {
            print(reg)
        }
        for (reg2 in regulon_names) {
            f <- f + 1

            fraction_lower <- calc_csi(reg, reg2, pearson_cor)

            csi_regulons[f, ] <- c(reg, reg2, fraction_lower)
        }
    }
    csi_regulons$CSI <- as.numeric(csi_regulons$CSI)
    return(csi_regulons)
}