## ----, echo = FALSE, message = FALSE-------------------------------------
library(markdown)
options(markdown.HTML.options = c(options('markdown.HTML.options')[[1]], "toc"))

library(knitr)
knitr::opts_chunk$set(
    error = FALSE,
    tidy  = FALSE,
    message = FALSE,
    fig.align = "center")
options(markdown.HTML.stylesheet = "custom.css")

options(width = 100)

## ----, echo = FALSE, message = FALSE-------------------------------------
suppressPackageStartupMessages(library(EnrichedHeatmap))

## ----, eval = FALSE------------------------------------------------------
## library(EnrichedHeatmap)

## ------------------------------------------------------------------------
set.seed(123)
load(paste0(system.file("extdata", "chr21_test_data.RData", package = "EnrichedHeatmap")))
ls()

## ----h3k4me3, fig.width = 3----------------------------------------------
tss = promoters(genes, upstream = 0, downstream = 1)
tss[1:5]
H3K4me3[1:5]
mat1 = normalizeToMatrix(H3K4me3, tss, value_column = "coverage", 
    extend = 5000, mean_mode = "w0", w = 50)
mat1
EnrichedHeatmap(mat1, name = "H3K4me3")

## ----anno, fig.width = 3-------------------------------------------------
EnrichedHeatmap(mat1, col = c("white", "red"), name = "H3K4me3",
    top_annotation = HeatmapAnnotation(lines = anno_enriched()), 
    top_annotation_height = unit(2, "cm"))

## ----smooth, fig.width = 3-----------------------------------------------
library(circlize)
mat1_smoothed = normalizeToMatrix(H3K4me3, tss, value_column = "coverage", 
    extend = 5000, mean_mode = "w0", w = 50, smooth = TRUE)
# note we set the color range same as the unsmoothed matrix
EnrichedHeatmap(mat1_smoothed, col = colorRamp2(range(mat1), c("white", "red")), 
    name = "H3K4me3")

## ----split, fig.width = 3------------------------------------------------
EnrichedHeatmap(mat1, col = c("white", "red"), name = "H3K4me3", 
    split = sample(c("A", "B"), length(genes), replace = TRUE),
    column_title = "Enrichment of H3K4me3") 

## ----kmeans, fig.width = 4-----------------------------------------------
EnrichedHeatmap(mat1, col = c("white", "red"), name = "H3K4me3", km = 3,
    column_title = "Enrichment of H3K4me3", row_title_rot = 0)

## ----, kmeans_anno, fig.width = 4----------------------------------------
EnrichedHeatmap(mat1, col = c("white", "red"), name = "H3K4me3",
    # note we have three row-clusters, so we assign three colors for the annotation lines
    top_annotation = HeatmapAnnotation(lines = anno_enriched(gp = gpar(col = 2:4))), 
    top_annotation_height = unit(2, "cm"),
    km = 3, row_title_rot = 0)

## ----, cluster, fig.width = 3--------------------------------------------
EnrichedHeatmap(mat1, col = c("white", "red"), name = "H3K4me3", 
    cluster_rows = TRUE, show_row_dend = FALSE, column_title = "Enrichment of H3K4me3")     

## ----aixs, fig.width = 3-------------------------------------------------
EnrichedHeatmap(mat1, col = c("white", "red"), name = "H3K4me3", 
    pos_line_gp = gpar(col = "blue", lwd = 2), axis_name = c("-5kb", "TSS", "5kb"), 
    axis_name_rot = -45, border = FALSE)

## ----extend, fig.width = 3-----------------------------------------------
# upstream 1kb, downstream 2kb
mat12 = normalizeToMatrix(H3K4me3, tss, value_column = "coverage", 
    extend = c(1000, 2000), mean_mode = "w0", w = 50)
EnrichedHeatmap(mat12, name = "H3K4me3", col = c("white", "red"))

## ----meth, fig.width = 3-------------------------------------------------
meth[1:5]
mat2 = normalizeToMatrix(meth, tss, value_column = "meth", mean_mode = "absolute",
    extend = 5000, w = 50, empty_value = 0.5)
EnrichedHeatmap(mat2, name = "methylation", column_title = "methylation near TSS")

## ----meth2, fig.width = 3------------------------------------------------
mat2 = normalizeToMatrix(meth, tss, value_column = "meth", mean_mode = "absolute",
    extend = 5000, w = 50, empty_value = NA, smooth = TRUE)
EnrichedHeatmap(mat2, name = "methylation", column_title = "methylation near TSS")

## ----cgi, fig.width = 3--------------------------------------------------
mat3 = normalizeToMatrix(meth, cgi, value_column = "meth", mean_mode = "absolute",
    extend = 5000, w = 50, empty_value = NA, smooth = TRUE)
EnrichedHeatmap(mat3, name = "methylation", column_title = "methylation near CGI")

## ----fat_cgi, fig.width = 3----------------------------------------------
mat3 = normalizeToMatrix(meth, cgi, value_column = "meth", mean_mode = "absolute",
    extend = 5000, w = 50, empty_value = NA, smooth = TRUE, target_ratio = 0.3)
EnrichedHeatmap(mat3, name = "methylation", axis_name_rot = 90,
    column_title = "methylation near CGI")

## ----list, fig.width = 6-------------------------------------------------
EnrichedHeatmap(mat1, col = c("white", "red"), name = "H3K4me3", width = 1) + 
EnrichedHeatmap(mat2, name = "methylation", width = 1) +
Heatmap(log2(rpkm+1), col = c("white", "orange"), name = "log2(rpkm+1)", 
    show_row_names = FALSE, width = unit(5, "mm"))

## ----list_split, fig.width = 7-------------------------------------------
EnrichedHeatmap(mat1, col = c("white", "red"), name = "H3K4me3", km = 3, width = 1,
    top_annotation = HeatmapAnnotation(lines = anno_enriched()), 
    top_annotation_height = unit(2, "cm"), row_title_rot = 0,
    column_title = "H3K4me3") + 
EnrichedHeatmap(mat2, name = "methylation", width = 1,
    column_title = "Methylation") +
Heatmap(log2(rpkm+1), col = c("white", "orange"), name = "log2(rpkm+1)", 
    show_row_names = FALSE, width = unit(5, "mm"))

## ------------------------------------------------------------------------
load(paste0(system.file("/extdata/neg_cr.RData", package = "EnrichedHeatmap")))
all_tss = promoters(all_genes, upstream = 0, downstream = 1)
all_tss = all_tss[unique(neg_cr$gene)]
neg_cr
all_tss

## ----neg_cr, fig.width = 3-----------------------------------------------
mat4 = normalizeToMatrix(neg_cr, all_tss, mapping_column = "gene", w = 50, mean_mode = "w0")
EnrichedHeatmap(mat4, col = c("white", "green"), name = "neg_cr", cluster_rows = TRUE,
    top_annotation = HeatmapAnnotation(lines = anno_enriched(gp = gpar(col = "green"))), 
    top_annotation_height = unit(2, "cm"))

## ----neg_cr_with_tx, fig.width = 6---------------------------------------
mat5 = normalizeToMatrix(tx, all_tss, mapping_column="gene", w = 50, mean_mode = "w0")
ht_list = EnrichedHeatmap(mat4, col = c("white", "green"), name = "neg_cr", cluster_rows = TRUE,
              top_annotation = HeatmapAnnotation(lines1 = anno_enriched(gp = gpar(col = "green"))), 
              top_annotation_height = unit(2, "cm")) +
          EnrichedHeatmap(mat5, col = c("white", "black"), name = "tx",
              top_annotation = HeatmapAnnotation(lines2 = anno_enriched(gp = gpar(col = "black"))), 
              top_annotation_height = unit(2, "cm"))
draw(ht_list, gap = unit(1, "cm"))

## ----, eval = FALSE------------------------------------------------------
## ht_list = draw(ht_list)
## row_order(ht_list)

## ----, eval = FALSE------------------------------------------------------
## draw(ht_list)
## pos = select()

## ----, eval = FALSE------------------------------------------------------
## EnrichedHeatmap(..., column_title_gp = ...)

## ----, eval = FALSE------------------------------------------------------
## EnrichedHeatmap(..., heatmap_legend_param = ...)
## # or set is globally
## ht_global_opt(...)
## EnrichedHeatmap(...)
## ht_global_opt(RESET = TRUE)

## ----, eval = FALSE------------------------------------------------------
## EnrichedHeatmap(..., width = unit(...)) + EnrichedHeatmap(...)

## ------------------------------------------------------------------------
sessionInfo()