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R/Plot_heatmap/Heatmapper.R

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+library(GenomicRanges)
+library(dynamicTreeCut)
+library(ComplexHeatmap)
+library(circlize)
+library(RColorBrewer)
+library(ChIPseeker)
+library(TxDb.Hsapiens.UCSC.hg19.knownGene)
+library(ggplot2)
+library(data.table)
+
+source("Heatmapper_functions.R")
+
+
+bwfile = c("../../SCLC_NAPY_ChIP/NA_chip/bigwigs/GSM1700639_H889_ASCL1.scaled.bw",
+           "../../SCLC_NAPY_ChIP/NA_chip/bigwigs/GSM1700641_H82_NEUROD1.scaled.bw",
+           "/Volumes/LMP/ngs/chip/SCLC_cell_lines/bigwigs_hg19_clean/NCI-H1048_POU2F3_rep1.hg19_clean.bam.scaled.bw",
+           "/Volumes/LMP/ngs/chip/SCLC_cell_lines/bigwigs_hg19_clean/NCI-H889_H3K27ac_rep1.hg19_clean.bam.scaled.bw",
+           "/Volumes/LMP/ngs/chip/SCLC_cell_lines/bigwigs_hg19_clean/NCI-H82_H3K27ac_rep1.hg19_clean.bam.scaled.bw",
+           "/Volumes/LMP/ngs/chip/SCLC_cell_lines/bigwigs_hg19_clean/NCI-H1048_H3K27ac_rep1.hg19_clean.bam.scaled.bw",
+           "/Volumes/LMP/ngs/chip/SCLC_cell_lines/bigwigs_hg19_clean/DMS114_H3K27ac_rep1.hg19_clean.bam.scaled.bw")
+
+peaks = c("Intervene_results/sets/100_ASCL1.bed",
+          "Intervene_results/sets/010_NEUROD1.bed",
+          "Intervene_results/sets/001_POU2F3.bed")
+
+bwnames = c("H889_ASCL1", "H82_NEUROD1", "H1048_POU2F3", "H889", "H82", "H1048", "DMS114")
+pnames = c("A", "N", "P")
+
+heatobj = ImportHeatMapperData(bedfiles = peaks,
+                               bednames = pnames,
+                               bwfiles = bwfile, 
+                               bwnames = bwnames, 
+                               extend_peaks = c(2500),
+                               subset_peaks = 1500, 
+                               individual_subsetting = 1)
+
+heatobj = PrepBEDheatmapdata(obj = heatobj, cluster = "no")
+heatobj = PrepHeatmapPlots(obj = heatobj,
+                           color_palette = c("Reds", "Greens", "Blues", "Purples", "Purples", "Purples", "Purples"),
+                           #lineplot_max_value = c(20), lineplot_min_value = c(10),
+                           split_colors = c("red", "green", "blue"), 
+                           raster_quality = 1, same_scale = 0)
+draw(heatobj@combined_heatmaps, ht_gap = unit(1, "cm"))
+