RNAseqSurgeryDiet/HigherLevelAnalysis.R at main · shnsk1995/RNAseqSurgeryDiet · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147


PlotPathwayHeatmaps <- function(tissueOfInterest,pathways,pathwayNames){


  readPath <- "data/FGSEAResults/"

  if(!dir.exists("data/HigherLevelAnalysis")){
    dir.create("data/HigherLevelAnalysis")
  }

  if(!dir.exists("data/HigherLevelAnalysis/PathwayHeatmaps")){
    dir.create("data/HigherLevelAnalysis/PathwayHeatmaps")
  }

  writePath <- "data/HigherLevelAnalysis/PathwayHeatmaps/"

  for (i in 1:length(pathwayNames)) {

    if(!dir.exists(paste0("data/HigherLevelAnalysis/PathwayHeatmaps/",pathwayNames[i]))){
      dir.create(paste0("data/HigherLevelAnalysis/PathwayHeatmaps/",pathwayNames[i]))
    }

    writePath <- paste0("data/HigherLevelAnalysis/PathwayHeatmaps/",pathwayNames[i],"/")

    contrasts <- c("HF_Surgery","LF_Surgery","Diet","Surgery","Surgery_Diet")

    for (contrast in contrasts){

      pathNames <- names(pathways[[i]])

      heatmapData <- as.data.frame(matrix(ncol = length(tissueOfInterest),nrow = length(pathNames)))

      rownames(heatmapData) <- pathNames
      colnames(heatmapData) <- tissueOfInterest

      for (tissue in tissueOfInterest) {

        fgseares <- read.xlsx(paste0(readPath,tissue,"/AllPathways.xlsx"),sheet = paste0(pathwayNames[i],"_",contrast))

        sigUpPathwayNames <- fgseares[fgseares$padj < 0.05 & fgseares$NES > 0,]$pathway
        sigDownPathwayNames <- fgseares[fgseares$padj < 0.05 & fgseares$NES < 0,]$pathway

        for (pathway in pathNames) {

          if(pathway %in% sigUpPathwayNames){
            heatmapData[pathway,tissue] <- 1
          }else if(pathway %in% sigDownPathwayNames){
            heatmapData[pathway,tissue] <- -1
          }else{
            heatmapData[pathway,tissue] <- 0
          }

        }


      }

      heatmapData <- heatmapData %>%
        dplyr::mutate(UpCount = rowSums(across(all_of(tissueOfInterest)) == 1))

      heatmapData <- heatmapData %>%
        dplyr::mutate(DownCount = rowSums(across(all_of(tissueOfInterest)) == -1))

      heatmapData <- heatmapData %>%
        dplyr::mutate(NoSigCount = rowSums(across(all_of(tissueOfInterest)) == 0))

      heatmapDataDf <- heatmapData[!heatmapData$NoSigCount==8,-(9:11)]

      colFun <- colorRamp2(c(-1, 0, 1), c("blue", "white", "red"))

      heatMap <- Heatmap(as.matrix(heatmapDataDf),
                         column_names_side = "top",
                         col = colFun,
                         border = TRUE,
                         row_names_gp = gpar(fontsize = 15),
                         column_names_gp = gpar(fontsize = 12),
                         heatmap_width = unit(28,"cm"),
                         heatmap_height = unit(40,"cm"),
                         show_heatmap_legend = FALSE,
                         rect_gp = gpar(col = "black", lwd = 1),
                         column_title =  paste0("Heatmap of significant pathways for ",contrast," contrast"),
                         column_title_gp = gpar(fontsize = 20, fontface = "bold")
      )

      lgd = Legend(
        labels = c("Up", "NotSig", "Down"),
        title = "Significance",
        legend_gp = gpar(fill = c("red", "white", "blue")),
        border = TRUE,
        direction = "horizontal",
        title_gp = gpar(fontsize = 15),
        labels_gp = gpar(fontsize = 15)
      )


      jpeg(paste0(writePath,pathwayNames[i],"_",contrast,"_PathwayHeatMap.jpeg"),height = 1400,width = 1600,quality = 100)
      draw(heatMap,annotation_legend_list = list(lgd),
           annotation_legend_side = "bottom"
      )
      dev.off()

      file <- paste0(writePath,pathwayNames[i],"_PathwaysSignificance.xlsx")

      if (file.exists(file)) {
        # Load the existing workbook
        wb <- loadWorkbook(file)


        sheetName <- contrast
        # Add a new sheet (check if the sheet already exists first)
        if (!(sheetName %in% names(wb))) {
          addWorksheet(wb, sheetName)
        }

        # Optionally, write some data to the new sheet
        writeData(wb, sheetName,heatmapData, startCol = 1, startRow = 1,rowNames = TRUE, colNames = TRUE)

        # Save the workbook
        saveWorkbook(wb, file, overwrite = TRUE)

      } else {

        # Create a new workbook if the file doesn't exist
        wb <- createWorkbook()

        # Add a new sheet
        sheetName <- contrast
        addWorksheet(wb, sheetName)

        # Optionally, write some data to the new sheet
        writeData(wb, sheetName,heatmapData, startCol = 1, startRow = 1,rowNames = TRUE, colNames = TRUE)

        # Save the new workbook
        saveWorkbook(wb, file, overwrite = TRUE)
      }

    }


  }


}