library(readr)
library(pheatmap)
library(cosmosR)
library(decoupleR)
library(GSEABase)

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## Welcome to Bioconductor
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##     'citation("Biobase")', and for packages 'citation("pkgname")'.

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full_moon_res_combined <- as.data.frame(
  read_csv("results/cosmos/moon/full_moon_res_combined.csv"))

## Rows: 3122 Columns: 3
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (1): source
## dbl (2): score, level
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combined_meta_network_translated <- as.data.frame(
  read_csv("results/cosmos/moon/combined_meta_network_translated.csv"))

## Rows: 14027 Columns: 3
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## chr (2): source, target
## dbl (1): interaction
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## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

background_nodes <- full_moon_res_combined[abs(full_moon_res_combined$score) > 1,"source"]

pathway_control_df <- reshape2::dcast(pathway_control_set, pathway~node_of_interest, value.var = "p-value")
row.names(pathway_control_df) <- pathway_control_df$pathway

pathway_control_df <- pathway_control_df[,-1]
pathway_control_df <- pathway_control_df[,apply(pathway_control_df, 2, function(x){min(x) < 0.1})]

threshold_pval <- 0.0000000000000001

pathway_control_df_top <- pathway_control_df[!grepl("CANCER",row.names(pathway_control_df)),]
pathway_control_df_top <- pathway_control_df_top[apply(pathway_control_df_top, 1, function(x){min(x) < threshold_pval}),apply(pathway_control_df_top, 2, function(x){min(x) < threshold_pval})]
pathway_control_df_top <- -log10(pathway_control_df_top)
# pathway_control_df_top[pathway_control_df_top < 3] <- NA
pathway_control_df_top[pathway_control_df_top >= 15] <- 15
pathway_control_df_top[pathway_control_df_top >= 8 & pathway_control_df_top < 15] <- 8
pathway_control_df_top[pathway_control_df_top >= 3 & pathway_control_df_top < 8] <- 3
pathway_control_df_top[pathway_control_df_top <3] <- 0

row.names(pathway_control_df_top) <- tolower(gsub("_"," ",gsub("KEGG","",row.names(pathway_control_df_top))))
names(pathway_control_df_top) <- gsub("Metab__","",gsub("_[a-z$]","",names(pathway_control_df_top)))
pheatmap::pheatmap(pathway_control_df_top, angle_col = 315, na_col = "grey", cluster_rows = T, cluster_cols = T, display_numbers = F, number_color = "black", color = colorRampPalette(c("white","red"))(100), treeheight_row = 0, treeheight_col = 0)

pheatmap::pheatmap(pathway_control_df_top, angle_col = 315, na_col = "grey", cluster_rows = T, cluster_cols = T, display_numbers = F, number_color = "black", color = colorRampPalette(c("white","red"))(100), treeheight_row = 0, treeheight_col = 0, filename = "results/cosmos/moon/pathway_control_top.pdf", height = 3, width = 9)