Nothing
## ---- message = FALSE---------------------------------------------------------
library("HiCBricks")
## -----------------------------------------------------------------------------
Bintable_path <- system.file(file.path("extdata",
"Bintable_100kb.bins"), package = "HiCBricks")
## ----echo = FALSE, results = "asis"-------------------------------------------
library(knitr)
kable(data.frame(chr = c("chr2L", "chr2R", "chr3L", "chr3R", "chrX"),
num_rows = c(231, 212, 246, 280, 225)),
caption = "Number of rows in the bintable corresponding to each chromosome")
## -----------------------------------------------------------------------------
out_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
dir.create(out_dir)
Create_many_Bricks(BinTable = Bintable_path,
bin_delim=" ", output_directory = out_dir,
file_prefix = "HiCBricks_vignette_test", remove_existing=TRUE,
experiment_name = "HiCBricks vignette test", resolution = 100000)
## -----------------------------------------------------------------------------
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Example_dataset_dir <- system.file("extdata", package = "HiCBricks")
Chromosomes <- c("chr2L", "chr3L", "chr3R", "chrX")
for (chr in Chromosomes) {
Matrix_file <- file.path(Example_dataset_dir,
paste(paste("Sexton2012_yaffetanay_CisTrans_100000_corrected",
chr, sep = "_"), "txt.gz", sep = "."))
Brick_load_matrix(Brick = My_BrickContainer,
chr1 = chr,
chr2 = chr,
resolution = 100000,
matrix_file = Matrix_file,
delim = " ",
remove_prior = TRUE)
}
## -----------------------------------------------------------------------------
Example_dataset_dir <- system.file("extdata", package = "HiCBricks")
Matrix_file <- file.path(Example_dataset_dir,
paste(paste("Sexton2012_yaffetanay_CisTrans_100000_corrected",
"chr2L", sep = "_"), "txt.gz", sep = "."))
Brick_load_cis_matrix_till_distance(Brick = My_BrickContainer,
chr = "chr2L",
resolution = 100000,
matrix_file = Matrix_file,
delim = " ",
distance = 100,
remove_prior = TRUE)
## ----eval = FALSE-------------------------------------------------------------
# require(curl)
# ftp_location = "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104427/suppl"
#
# sparse_matrix_file = file.path(ftp_location,"GSE104427_c2c12_40000_iced.matrix.gz")
# sparse_out_dir <- file.path(tempdir(), "sparse_out_dir")
# if(!dir.exists(sparse_out_dir)){
# dir.create(sparse_out_dir)
# }
# curl_download(url = sparse_matrix_file,
# destfile = file.path(sparse_out_dir, "GSE104427_c2c12_40000_iced.matrix.gz"))
#
# sparse_bintable_file = file.path(ftp_location,"GSE104427_c2c12_40000_abs.bed.gz")
# curl_download(url = sparse_matrix_file,
# destfile = file.path(sparse_out_dir, "GSE104427_c2c12_40000_abs.bed.gz"))
## ----eval = FALSE-------------------------------------------------------------
#
# Read_file_df <- read.table(file.path(sparse_out_dir, "GSE104427_c2c12_40000_iced.matrix.gz"))
# Read_file_df <- Read_file_df[Read_file_df[,2] >= Read_file_df[,1],]
# write.table(x = Read_file_df, file = file.path(sparse_out_dir, "GSE104427_c2c12_40000_iced_uppertri.matrix"),
# quote = FALSE, sep = " ", row.names = FALSE, col.names = FALSE)
#
## ----eval = FALSE-------------------------------------------------------------
#
# Read_bintable_df <- read.table(file.path(sparse_out_dir, "GSE104427_c2c12_40000_abs.bed.gz"))
# Read_bintable_df[,2] <- Read_bintable_df[,2] + 1
# write.table(x = Read_bintable_df[, c(1, 2, 3)], file = file.path(sparse_out_dir, "GSE104427_c2c12_40000_abs_discontinuous.bed"),
# quote = FALSE, sep = " ", row.names = FALSE, col.names = FALSE)
#
## ----eval = FALSE-------------------------------------------------------------
#
# Bintable_path <- file.path(sparse_out_dir, "GSE104427_c2c12_40000_abs_discontinuous.bed")
#
# My_sparse_brick_object <- Create_many_Bricks(BinTable = Bintable_path,
# bin_delim=" ", output_directory = out_dir,
# file_prefix = "HiCBricks_vignette_test", remove_existing=TRUE,
# experiment_name = "HiCBricks vignette test", resolution = 40000)
#
# Matrix_path <- file.path(sparse_out_dir, "GSE104427_c2c12_40000_iced_uppertri.matrix")
#
# Load_all_sparse <- Brick_load_data_from_sparse(Brick = My_sparse_brick_object,
# table_file = Matrix_path, delim = " ", resolution = 40000)
#
## ----eval = FALSE-------------------------------------------------------------
# require(curl)
# Consortium.home = "https://data.4dnucleome.org/files-processed"
# File = file.path(Consortium.home, "4DNFI7JNCNFB",
# "@@download","4DNFI7JNCNFB.mcool")
# mcool_out_dir <- file.path(tempdir(), "mcool_out_dir")
# dir.create(mcool_out_dir)
# curl_download(url = File,
# destfile = file.path(mcool_out_dir, "H1-hESC-HiC-4DNFI7JNCNFB.mcool"))
## ----eval = FALSE-------------------------------------------------------------
#
# mcool_out_dir <- file.path(tempdir(), "mcool_out_dir")
# mcool_path=file.path(mcool_out_dir, "H1-hESC-HiC-4DNFI7JNCNFB.mcool")
# Brick_list_mcool_resolutions(mcool = mcool_path)
#
## ----eval = FALSE-------------------------------------------------------------
#
# mcool_out_dir <- file.path(tempdir(), "mcool_out_dir")
# mcool_path=file.path(mcool_out_dir, "H1-hESC-HiC-4DNFI7JNCNFB.mcool")
# Brick_mcool_normalisation_exists(mcool = mcool_path,
# norm_factor = "Iterative-Correction",
# resolution = 10000)
#
## ----eval = FALSE-------------------------------------------------------------
#
# mcool_out_dir <- file.path(tempdir(), "mcool_out_dir")
# mcool_path=file.path(mcool_out_dir, "H1-hESC-HiC-4DNFI7JNCNFB.mcool")
#
# out_dir <- file.path(tempdir(), "mcool_to_Brick_test")
# dir.create(out_dir)
#
# Create_many_Bricks_from_mcool(output_directory = out_dir,
# file_prefix = "mcool_to_Brick_test",
# mcool = mcool_path,
# resolution = 10000,
# experiment_name = "Testing mcool creation",
# remove_existing = TRUE)
#
## ----eval = FALSE-------------------------------------------------------------
#
# mcool_out_dir <- file.path(tempdir(), "mcool_out_dir")
# mcool_path=file.path(mcool_out_dir, "H1-hESC-HiC-4DNFI7JNCNFB.mcool")
#
# out_dir <- file.path(tempdir(), "mcool_to_Brick_test")
#
# Create_many_Bricks_from_mcool(output_directory = out_dir,
# file_prefix = "mcool_to_Brick_test",
# mcool = mcool_path,
# resolution = 40000,
# experiment_name = "Testing mcool creation",
# remove_existing = TRUE)
#
## ----eval = FALSE-------------------------------------------------------------
#
# out_dir <- file.path(tempdir(), "mcool_to_Brick_test")
# My_BrickContainer <- load_BrickContainer(project_dir = out_dir)
#
# mcool_out_dir <- file.path(tempdir(), "mcool_out_dir")
# mcool_path=file.path(mcool_out_dir, "H1-hESC-HiC-4DNFI7JNCNFB.mcool")
#
# Brick_load_data_from_mcool(Brick = My_BrickContainer,
# mcool = mcool_path,
# resolution = 10000,
# cooler_read_limit = 10000000,
# matrix_chunk = 2000,
# remove_prior = TRUE,
# norm_factor = "Iterative-Correction")
#
## ----eval = FALSE-------------------------------------------------------------
#
# # load the Brick Container
# BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
# My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
#
# # export the contact matrix to a a sparse matrix format and save it on a file
# Brick_export_to_sparse(Brick=My_BrickContainer,
# out_file="brick_export.tsv",
# remove_file=TRUE,
# resolution=100000,
# sep="\t")
#
# # create a dataframe containing the bintable
# bintable<-Brick_get_bintable(My_BrickContainer, resolution = 100000)
#
# require(GenomicRanges)
#
# df1<-data.frame(seqnames=seqnames(bintable),
# start(bintable)-1,
# ends=end(bintable),
# names=c(rep(".",length(bintable))),
# scores=c(rep(".", length(bintable))),
# strands=strand(bintable))
#
# # save the bintable as a bed file
# write.table(df1,
# file="bintable.bed",
# quote=FALSE,
# row.names=FALSE,
# col.names=FALSE,
# sep="\t")
## ----eval = FALSE-------------------------------------------------------------
#
# sed -e "1d" brick_export.tsv | cut -f3-5 > exported_bins_no_header.tsv
#
## ----eval = FALSE-------------------------------------------------------------
#
# cooler load -f coo \
# --count-as-float \
# --one-based \
# bintable.bed \
# exported_bins_no_header.tsv \
# test_cool_from_hicbricks.cool
#
## ----eval = FALSE-------------------------------------------------------------
#
# cooler zoomify -p 1 \
# -r 200000,500000 \
# -o 2_test_cool_from_hicbricks.mcool \
# test_cool_from_hicbricks.cool
#
## -----------------------------------------------------------------------------
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Brick_list_rangekeys(Brick = My_BrickContainer, resolution = 100000)
## -----------------------------------------------------------------------------
BrickContainer_file <- file.path(tempdir(),
"HiCBricks_vignette_test", "HiCBricks_builder_config.json")
My_BrickContainer <- load_BrickContainer(config_file = BrickContainer_file)
Brick_get_bintable(My_BrickContainer, resolution = 100000)
## -----------------------------------------------------------------------------
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Brick_get_ranges(Brick = My_BrickContainer,
rangekey = "Bintable", resolution = 100000)
## -----------------------------------------------------------------------------
BrickContainer_file <- file.path(tempdir(), "HiCBricks_vignette_test",
"HiCBricks_builder_config.json")
My_BrickContainer <- load_BrickContainer(config_file = BrickContainer_file)
Brick_get_ranges(Brick = My_BrickContainer,
rangekey = "Bintable",
chr = "chr3R",
resolution = 100000)
## -----------------------------------------------------------------------------
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Brick_return_region_position(Brick = My_BrickContainer,
region = "chr2L:5000000:10000000", resolution = 100000)
## -----------------------------------------------------------------------------
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Brick_fetch_range_index(Brick = My_BrickContainer,
chr = "chr2L",
start = 5000000,
end = 10000000, resolution = 100000)
## -----------------------------------------------------------------------------
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Values <- Brick_get_values_by_distance(Brick = My_BrickContainer,
chr = "chr2L",
distance = 4, resolution = 100000)
## -----------------------------------------------------------------------------
Failsafe_median_log10 <- function(x){
x[is.nan(x) | is.infinite(x) | is.na(x)] <- 0
return(median(log10(x+1)))
}
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Brick_get_values_by_distance(Brick = My_BrickContainer,
chr = "chr2L",
distance = 4, resolution = 100000,
FUN = Failsafe_median_log10)
## -----------------------------------------------------------------------------
Failsafe_median_log10 <- function(x){
x[is.nan(x) | is.infinite(x) | is.na(x)] <- 0
return(median(log10(x+1)))
}
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Brick_get_values_by_distance(Brick = My_BrickContainer,
chr = "chr2L",
distance = 4,
constrain_region = "chr2L:1:5000000",
resolution = 100000,
FUN = Failsafe_median_log10)
## -----------------------------------------------------------------------------
Sub_matrix <- Brick_get_matrix_within_coords(Brick = My_BrickContainer,
x_coords="chr2L:5000000:10000000",
force = TRUE,
resolution = 100000,
y_coords = "chr2L:5000000:10000000")
dim(Sub_matrix)
## -----------------------------------------------------------------------------
x_axis <- 5000000/100000
y_axis <- 10000000/100000
Sub_matrix <- Brick_get_matrix(Brick = My_BrickContainer,
chr1 = "chr3R", chr2 = "chr3R", resolution = 100000,
x_coords = seq(from = x_axis, to = y_axis),
y_coords = seq(from = x_axis, to = y_axis))
dim(Sub_matrix)
## -----------------------------------------------------------------------------
Coordinate <- c("chr3R:1:100000","chr3R:100001:200000")
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Test_Run <- Brick_fetch_row_vector(Brick = My_BrickContainer,
chr1 = "chr3R",
chr2 = "chr3R",
by = "ranges",
resolution = 100000,
vector = Coordinate)
## -----------------------------------------------------------------------------
Coordinate <- c(1,2)
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Test_Run <- Brick_fetch_row_vector(Brick = My_BrickContainer,
chr1 = "chr3R",
chr2 = "chr3R",
by = "position",
resolution = 100000,
vector = Coordinate)
## -----------------------------------------------------------------------------
Coordinate <- c(1,2)
Test_Run <- Brick_fetch_row_vector(Brick = My_BrickContainer,
chr1 = "chr3R",
chr2 = "chr3R",
by = "position",
vector = Coordinate,
resolution = 100000,
regions = c("chr3R:1:1000000", "chr3R:100001:2000000"))
## -----------------------------------------------------------------------------
Brick_list_matrix_mcols()
## -----------------------------------------------------------------------------
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
MCols.dat <- Brick_get_matrix_mcols(Brick = My_BrickContainer,
chr1 = "chr3R",
chr2 = "chr3R",
resolution = 100000,
what = "chr1_row_sums")
head(MCols.dat, 100)
## -----------------------------------------------------------------------------
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Brick_matrix_isdone(Brick = My_BrickContainer,
chr1 = "chr3R",
chr2 = "chr3R",
resolution = 100000)
## -----------------------------------------------------------------------------
Brick_matrix_issparse(Brick = My_BrickContainer,
chr1 = "chr2L",
chr2 = "chr2L",
resolution = 100000)
## -----------------------------------------------------------------------------
Brick_matrix_maxdist(Brick = My_BrickContainer,
chr1 = "chr2L",
chr2 = "chr2L",
resolution = 100000)
## -----------------------------------------------------------------------------
Brick_matrix_exists(Brick = My_BrickContainer,
chr1 = "chr2L",
chr2 = "chr2L",
resolution = 100000)
## -----------------------------------------------------------------------------
Brick_matrix_minmax(Brick = My_BrickContainer,
chr1 = "chr2L",
chr2 = "chr2L",
resolution = 100000)
## -----------------------------------------------------------------------------
Brick_matrix_dimensions(Brick = My_BrickContainer,
chr1 = "chr2L",
chr2 = "chr2L",
resolution = 100000)
## -----------------------------------------------------------------------------
Brick_matrix_filename(Brick = My_BrickContainer,
chr1 = "chr2L",
chr2 = "chr2L",
resolution = 100000)
## -----------------------------------------------------------------------------
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Chromosome <- c("chr2L", "chr3L", "chr3R", "chrX")
di_window <- 10
lookup_window <- 30
TAD_ranges <- Brick_local_score_differentiator(Brick = My_BrickContainer,
chrs = Chromosome,
resolution = 100000,
di_window = di_window,
lookup_window = lookup_window,
strict = TRUE,
fill_gaps = TRUE,
chunk_size = 500)
## -----------------------------------------------------------------------------
Name <- paste("LSD",
di_window,
lookup_window, sep = "_")
Brick_add_ranges(Brick = My_BrickContainer,
ranges = TAD_ranges,
rangekey = Name,
resolution = 100000)
## -----------------------------------------------------------------------------
Brick_list_rangekeys(Brick = My_BrickContainer, resolution = 100000)
TAD_ranges <- Brick_get_ranges(Brick = My_BrickContainer, rangekey = Name,
resolution = 100000)
## ----plot, fig.cap = "A normal heatmap without any transformations", fig.small = TRUE----
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-normal.pdf"),
Bricks = list(My_BrickContainer),
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
palette = "Reds",
width = 10,
height = 11,
return_object=TRUE)
## ----plot2, fig.cap = "A normal heatmap with colours computed in log10 scale", fig.small = TRUE----
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Failsafe_log10 <- function(x){
x[is.na(x) | is.nan(x) | is.infinite(x)] <- 0
return(log10(x+1))
}
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-normal-colours-log10.pdf"),
Bricks = list(My_BrickContainer),
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
FUN = Failsafe_log10,
legend_title = "Log10 Hi-C signal",
palette = "Reds",
width = 10,
height = 11,
return_object=TRUE)
## ----plot3, fig.cap = "A normal heatmap with colours computed in log10 scale after capping values to the 99th percentile", fig.small = TRUE----
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-normal-colours-log10-valuecap-99.pdf"),
Bricks = list(My_BrickContainer),
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
FUN = Failsafe_log10,
value_cap = 0.99,
legend_title = "Log10 Hi-C signal",
palette = "Reds",
width = 10,
height = 11,
return_object = TRUE)
## ----plot4, fig.cap = "Same heatmap as before with colours computed in log10 scale after capping values to the 99th percentile with 45 degree rotation", fig.small = TRUE----
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-normal-colours-log10-rotate.pdf"),
Bricks = list(My_BrickContainer),
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
FUN = Failsafe_log10,
value_cap = 0.99,
distance = 60,
legend_title = "Log10 Hi-C signal",
palette = "Reds",
width = 10,
height = 11,
rotate = TRUE,
return_object = TRUE)
## ----plot5, fig.cap = "Same heatmap as previous, but now the heatmaps are wider than they are taller", fig.wide = TRUE----
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-normal-colours-log10-rotate-2.pdf"),
Bricks = list(My_BrickContainer),
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
FUN = Failsafe_log10,
value_cap = 0.99,
distance = 60,
legend_title = "Log10 Hi-C signal",
palette = "Reds",
width = 15,
height = 5,
rotate = TRUE,
return_object = TRUE)
## ----plot6, fig.cap = "Normal rectangular heatmap with colours computed in the log scale after capping values to the 99th percentile with TAD calls", fig.small = TRUE----
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-normal-colours-log10-rotate-2-tads.pdf"),
Bricks = list(My_BrickContainer),
tad_ranges = TAD_ranges,
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
colours = "#230C0F",
FUN = Failsafe_log10,
value_cap = 0.99,
legend_title = "Log10 Hi-C signal",
palette = "Reds",
width = 10,
height = 11,
return_object = TRUE)
## ----plot7, fig.cap = "Normal rotated heatmap with colours computed in the log scale after capping values to the 99th percentile with TAD calls", fig.wide = TRUE----
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-normal-colours-log10-rotate-3-tads.pdf"),
Bricks = list(My_BrickContainer),
tad_ranges = TAD_ranges,
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
colours = "#230C0F",
FUN = Failsafe_log10,
value_cap = 0.99,
distance = 60,
legend_title = "Log10 Hi-C signal",
palette = "Reds",
width = 15,
height = 5,
line_width = 0.8,
cut_corners = TRUE,
rotate = TRUE,
return_object=TRUE)
## ----plot8, fig.cap = "A normal two sample heatmap with colours computed in log10 scale after capping values to the 99th percentile", fig.small = TRUE----
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-bipartite-colours-log10-valuecap-99.pdf"),
Bricks = list(My_BrickContainer, My_BrickContainer),
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
FUN = Failsafe_log10,
value_cap = 0.99,
legend_title = "Log10 Hi-C signal",
palette = "YlGnBu",
width = 10,
height = 11,
return_object = TRUE)
## ----plot9, fig.cap = "A normal two sample heatmap with colours computed in log10 scale on values until the 30th diagonal and capping these values to the 99th percentile.", fig.small = TRUE----
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-bipartite-colours-log10-valuecap-99-2.pdf"),
Bricks = list(My_BrickContainer, My_BrickContainer),
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
FUN = Failsafe_log10,
value_cap = 0.99,
legend_title = "Log10 Hi-C signal",
palette = "RdGy",
distance = 30,
width = 10,
height = 11,
return_object = TRUE)
## ----plot10, fig.cap = "A rotated two sample heatmap with colours computed in log10 scale and capping these values to the 99th percentile.", fig.wide = TRUE----
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-bipartite-colours-log10-valuecap-99-rotate.pdf"),
Bricks = list(My_BrickContainer, My_BrickContainer),
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
FUN = Failsafe_log10,
value_cap = 0.99,
legend_title = "Log10 Hi-C signal",
palette = "YlGnBu",
distance = 30,
width = 15,
height = 4,
rotate = TRUE,
return_object = TRUE)
## -----------------------------------------------------------------------------
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Chromosome <- "chr3R"
di_windows <- c(5,10)
lookup_windows <- c(10, 20)
for (i in seq_along(di_windows)) {
di_window <- di_windows[i]
lookup_window <- lookup_windows[i]
TAD_ranges <- Brick_local_score_differentiator(Brick = My_BrickContainer,
chrs = Chromosome,
resolution = 100000,
di_window = di_window,
lookup_window = lookup_window,
strict = TRUE,
fill_gaps=TRUE,
chunk_size = 500)
Name <- paste("LSD",
di_window,
lookup_window,
Chromosome,sep = "_")
Brick_add_ranges(Brick = My_BrickContainer, ranges = TAD_ranges,
resolution = 100000, rangekey = Name)
}
## -----------------------------------------------------------------------------
Chromosome <- "chr3R"
di_windows <- c(5,10)
lookup_windows <- c(10, 20)
TADs_list <- list()
for (i in seq_along(di_windows)) {
di_window <- di_windows[i]
lookup_window <- lookup_windows[i]
Name <- paste("LSD",
di_window,
lookup_window,
Chromosome,sep = "_")
TAD_ranges <- Brick_get_ranges(Brick = My_BrickContainer,
resolution = 100000, rangekey = Name)
# Map TADs to their Hi-C maps
TAD_ranges$group <- i
# Map TADs to a specific categorical value for the colours
TAD_ranges$colour_group <- paste("LSD", di_window, lookup_window,
sep = "_")
TADs_list[[Name]] <- TAD_ranges
}
TADs_ranges <- do.call(c, unlist(TADs_list, use.names = FALSE))
## ----plot11, fig.cap = "A normal two sample heatmap with colours computed in log10 scale and capping these values to the 97th percentile, with TAD borders", fig.small = TRUE----
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Colours <- c("#B4436C", "#F78154")
Colour_names <- unique(TADs_ranges$colour_group)
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-bipartite-colours-log10-valuecap-99-tads.pdf"),
Bricks = list(My_BrickContainer, My_BrickContainer),
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
FUN = Failsafe_log10,
value_cap = 0.97,
legend_title = "Log10 Hi-C signal",
palette = "YlGnBu",
tad_ranges = TADs_ranges,
group_col = "group",
tad_colour_col = "colour_group",
colours = Colours,
colours_names = Colour_names,
distance = 30,
width = 9,
height = 11,
return_object=TRUE)
## ----plot12, fig.cap = "A rotated two sample heatmap with colours computed in log10 scale and capping these values to the 97th percentile, with non-truncated TAD borders", fig.wide = TRUE----
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Colours <- c("#B4436C", "#F78154")
Colour_names <- unique(TADs_ranges$colour_group)
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-bipartite-colours-log10-valuecap-99-rotate-tads.pdf"),
Bricks = list(My_BrickContainer, My_BrickContainer),
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
FUN = Failsafe_log10,
value_cap = 0.97,
legend_title = "Log10 Hi-C signal",
palette = "YlGnBu",
tad_ranges = TADs_ranges,
group_col = "group",
tad_colour_col = "colour_group",
colours = Colours,
colours_names = Colour_names,
distance = 30,
width = 15,
height = 4,
rotate = TRUE,
return_object=TRUE)
## ----plot13, fig.cap = "A rotated two sample heatmap with colours computed in log10 scale and capping these values to the 97th percentile, with truncated TAD borders", fig.wide = TRUE----
BrickContainer_dir <- file.path(tempdir(), "HiCBricks_vignette_test")
My_BrickContainer <- load_BrickContainer(project_dir = BrickContainer_dir)
Colours <- c("#B4436C", "#F78154")
Colour.names <- unique(TADs_ranges$colour_group)
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-bipartite-colours-log10-valuecap-99-rotate-tads-2.pdf"),
Bricks = list(My_BrickContainer, My_BrickContainer),
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
FUN = Failsafe_log10,
value_cap = 0.97,
legend_title = "Log10 Hi-C signal",
palette = "YlGnBu",
tad_ranges = TADs_ranges,
group_col = "group",
tad_colour_col = "colour_group",
colours = Colours,
colours_names = Colour_names,
distance = 30,
width = 15,
height = 4,
cut_corners = TRUE,
rotate = TRUE,
return_object=TRUE)
## ----plot14, fig.cap = "A rotated two sample heatmap with colours computed in log10 scale and capping these values to the 99th percentile.", fig.wide = TRUE----
Brick_vizart_plot_heatmap(File = file.path(tempdir(),
"chr3R-1-10MB-bipartite-final.pdf"),
Bricks = list(My_BrickContainer, My_BrickContainer),
x_coords = "chr3R:1:10000000",
y_coords = "chr3R:1:10000000",
resolution = 100000,
FUN = Failsafe_log10,
value_cap = 0.99,
legend_title = "Log10 Hi-C signal",
palette = "YlGnBu",
tad_ranges = TADs_ranges,
group_col = "group",
tad_colour_col = "colour_group",
colours = Colours,
colours_names = Colour.names,
distance = 30,
width = 15,
height = 4,
legend_key_width = unit(10, "mm"),
legend_key_height = unit(5, "mm"),
line_width = 1.2,
cut_corners = TRUE,
rotate = TRUE,
return_object=TRUE)
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