## ---- 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()

## ---- 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
class(mat1)

## ---- fig.width = 3------------------------------------------------------
EnrichedHeatmap(mat1, name = "H3K4me3")

## ---- fig.width = 3------------------------------------------------------
EnrichedHeatmap(mat1, col = c("white", "red"), name = "H3K4me3")

## ------------------------------------------------------------------------
quantile(H3K4me3$coverage, c(0, 0.25, 0.5, 0.75, 0.99, 1))
quantile(mat1, c(0, 0.25, 0.5, 0.75, 0.99, 1))

## ---- fig.width = 3------------------------------------------------------
mat1_trim = normalizeToMatrix(H3K4me3, tss, value_column = "coverage", 
    extend = 5000, mean_mode = "w0", w = 50, trim = c(0, 0.01))
EnrichedHeatmap(mat1_trim, col = c("white", "red"), name = "H3K4me3")

## ---- fig.width = 3------------------------------------------------------
library(circlize)
col_fun = colorRamp2(quantile(mat1, c(0, 0.99)), c("white", "red"))
EnrichedHeatmap(mat1, col = col_fun, name = "H3K4me3")

## ------------------------------------------------------------------------
mat1 = mat1_trim

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

## ---- fig.width = 4------------------------------------------------------
set.seed(123)
EnrichedHeatmap(mat1, col = col_fun, name = "H3K4me3", km = 3,
    column_title = "Enrichment of H3K4me3", row_title_rot = 0)

## ---- fig.width = 3------------------------------------------------------
EnrichedHeatmap(mat1, col = col_fun, name = "H3K4me3", 
    cluster_rows = TRUE, column_title = "Enrichment of H3K4me3")     

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

## ---- kmeans_anno, fig.width = 4-----------------------------------------
set.seed(123)
EnrichedHeatmap(mat1, col = col_fun, 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)

## ---- fig.width = 4------------------------------------------------------
set.seed(123)
lgd = Legend(at = c("cluster1", "cluster2", "cluster3"), title = "Clusters", 
    type = "lines", legend_gp = gpar(col = 2:4))
ht = EnrichedHeatmap(mat1, col = col_fun, 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), show_error = TRUE)), 
    top_annotation_height = unit(2, "cm"),
    km = 3, row_title_rot = 0)
draw(ht, annotation_legend_list = list(lgd))

## ----smooth, fig.width = 3-----------------------------------------------
mat1_smoothed = normalizeToMatrix(H3K4me3, tss, value_column = "coverage", 
    extend = 5000, mean_mode = "w0", w = 50, empty_value = 0, smooth = TRUE)
EnrichedHeatmap(mat1_smoothed, col = col_fun, name = "H3K4me3")

## ---- 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 = col_fun)

## ---- fig.width = 3------------------------------------------------------
mat12 = normalizeToMatrix(H3K4me3, tss, value_column = "coverage", 
    extend = c(0, 2000), mean_mode = "w0", w = 50)
EnrichedHeatmap(mat12, name = "H3K4me3", col = col_fun)
mat12 = normalizeToMatrix(H3K4me3, tss, value_column = "coverage", 
    extend = c(1000, 0), mean_mode = "w0", w = 50)
EnrichedHeatmap(mat12, name = "H3K4me3", col = col_fun)

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

## ---- fig.width = 3------------------------------------------------------
meth[1:5]
mat2 = normalizeToMatrix(meth, tss, value_column = "meth", mean_mode = "absolute",
    extend = 5000, w = 50, empty_value = NA)
meth_col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red"))
EnrichedHeatmap(mat2, col = meth_col_fun, name = "methylation", column_title = "methylation near TSS")

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

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

## ----extension, fig.width = 3--------------------------------------------
mat3 = normalizeToMatrix(meth, cgi, value_column = "meth", mean_mode = "absolute",
    extend = c(0, 5000), w = 50, empty_value = NA, smooth = TRUE, target_ratio = 0.5)
EnrichedHeatmap(mat3, col = meth_col_fun, name = "methylation", axis_name_rot = 90,
    column_title = "methylation near CGI")
mat3 = normalizeToMatrix(meth, cgi, value_column = "meth", mean_mode = "absolute",
    extend = c(5000, 0), w = 50, empty_value = NA, smooth = TRUE, target_ratio = 0.5)
EnrichedHeatmap(mat3, col = meth_col_fun, name = "methylation", axis_name_rot = 90,
    column_title = "methylation near CGI")
mat3 = normalizeToMatrix(meth, cgi, value_column = "meth", mean_mode = "absolute",
    extend = 0, w = 50, empty_value = NA, smooth = TRUE, target_ratio = 1)
EnrichedHeatmap(mat3, col = meth_col_fun, name = "methylation", axis_name_rot = 90,
    column_title = "methylation near CGI")

## ------------------------------------------------------------------------
attr(mat3, "failed_rows")

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

## ---- fig.width = 7, fig.height = 8--------------------------------------
set.seed(123)
partition = kmeans(mat1, centers = 3)$cluster
lgd = Legend(at = c("cluster1", "cluster2", "cluster3"), title = "Clusters", 
    type = "lines", legend_gp = gpar(col = 2:4))
ht_list = Heatmap(partition, col = structure(2:4, names = as.character(1:3)), name = "partition",
              show_row_names = FALSE, width = unit(3, "mm")) +
          EnrichedHeatmap(mat1, col = col_fun, name = "H3K4me3", split = partition, width = 1,
              top_annotation = HeatmapAnnotation(lines = anno_enriched(gp = gpar(col = 2:4))), 
              top_annotation_height = unit(2, "cm"), row_title_rot = 0,
              column_title = "H3K4me3", combined_name_fun = NULL) + 
          EnrichedHeatmap(mat2, col = meth_col_fun, name = "methylation", width = 1,
              top_annotation = HeatmapAnnotation(lines = anno_enriched(gp = gpar(col = 2:4))), 
              top_annotation_height = unit(2, "cm"),
              column_title = "Methylation") +
          Heatmap(log2(rpkm+1), col = c("white", "orange"), name = "log2(rpkm+1)", 
              show_row_names = FALSE, width = unit(5, "mm"))
draw(ht_list, main_heatmap = "H3K4me3", gap = unit(c(2, 10, 2), "mm"),
    annotation_legend_list = list(lgd))

## ------------------------------------------------------------------------
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[1:2]
all_tss[1:2]

## ---- 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"))

## ---- fig.width = 6------------------------------------------------------
mat5 = normalizeToMatrix(tx, all_tss, mapping_column="gene", extend = c(5000, 10000), w = 50, 
    mean_mode = "coverage")
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-------------------------------------------------------
## # code not run
## ht_list = draw(ht_list)
## row_order(ht_list)

## ---- eval = FALSE-------------------------------------------------------
## # code not run
## draw(ht_list)
## pos = selectArea()

## ---- eval = FALSE-------------------------------------------------------
## # code not run
## EnrichedHeatmap(..., column_title_gp = ...)

## ---- eval = FALSE-------------------------------------------------------
## # code not run
## EnrichedHeatmap(..., heatmap_legend_param = ...)
## # or set is globally
## ht_global_opt(...)
## EnrichedHeatmap(...)
## ht_global_opt(RESET = TRUE)

## ---- eval = FALSE-------------------------------------------------------
## # code not run
## EnrichedHeatmap(..., width = ...) + EnrichedHeatmap(...)

## ---- eval = FALSE-------------------------------------------------------
## # code not run
## mat_list = NULL
## for(i in seq_along(hm_gr_list)) {
##     mat_list[[i]] = normalizeToMatrix(hm_gr_list[[i]], tss, value_column = ...)
## }

## ---- eval = FALSE-------------------------------------------------------
## # code not run
## mat = getSignalsFromList(mat_list)
## EnrichedHeatmap(mat)

## ---- eval = FALSE-------------------------------------------------------
## # code not run
## mat = getSignalsFromList(mat_list, fun = function(x, i) cor(x, expr[i, ], method = "spearman"))

## ---- eval = FALSE-------------------------------------------------------
## # code not run
## EnrichedHeatmap(mat)

## ---- eval = FALSE-------------------------------------------------------
## # code not run
## EnrichedHeatmap(mat, use_raster = TRUE, raster_device = ..., raster_device_param = ...)

## ---- eval = FALSE-------------------------------------------------------
## # code not run
## mat = normalizeToMatrix(..., smooth = FALSE)
## # the percent of NA values in each row
## apply(mat, 1, function(x) sum(is.na(x)/length(x)))

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