Brick_vizart_plot_heatmap: Create the entire HDF5 structure and load the bintable

In koustav-pal/HiCBricks: Framework for Storing and Accessing Hi-C Data Through HDF Files

Create the entire HDF5 structure and load the bintable

Description

Brick_vizart_plot_heatmap creates various heatmaps and plots TADs.

Usage

Brick_vizart_plot_heatmap(
    File,
    Bricks,
    resolution,
    x_coords,
    y_coords,
    FUN = NULL,
    value_cap = NULL,
    distance = NULL,
    rotate = FALSE,
    x_axis = TRUE,
    x_axis_title = NULL,
    y_axis = TRUE,
    y_axis_title = NULL,
    title = NULL,
    legend_title = NULL,
    return_object = FALSE,
    x_axis_num_breaks = 5,
    y_axis_num_breaks = 5,
    palette,
    col_direction = 1,
    extrapolate_on = NULL,
    x_axis_text_size = 10,
    y_axis_text_size = 10,
    text_size = 10,
    legend_title_text_size = 8,
    legend_text_size = 8,
    title_size = 10,
    tad_ranges = NULL,
    group_col = NULL,
    tad_colour_col = NULL,
    colours = NULL,
    colours_names = NULL,
    cut_corners = FALSE,
    highlight_points = NULL,
    width = 10,
    height = 6,
    line_width = 0.5,
    units = "cm",
    legend_key_width = unit(3, "cm"),
    legend_key_height = unit(0.5, "cm")
)

Arguments

File	Required A character vector containing the output filename to write.
Bricks	Required A list of length 1 (in case of one sample heatmaps) or 2 (in case of two sample heatmaps) specifying the BrickContainers from where to fetch the data.
resolution	Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed
x_coords	Required A character vector of length 1 specifying the coordinates from where to fetch the data.
y_coords	Required A character vector of length 1 specifying the coordinates from where to fetch the data.
FUN	Optional. Default NULL If any sort of transformations should be applied to the data before plotting. Such as, log10 or log2 transformations.
value_cap	Optional. Default NULL If present, values beyond a certain quantile will be capped to that quantile. In Hi-C this helps to emphasize structural information. Please note, if this parameter is present the greatest value will have a greater than sign append- -ed to them.
distance	Optional. Default NULL If present, values beyond this distance will be filtered out. Please note, that if a Brick store matrix was loaded until a certain distance, this parameter will result in an error if it is greater than the loaded distance.
rotate	Optional. Default FALSE If TRUE, will rotate the heatmap by 90 degrees.
x_axis	Optional. Default TRUE If FALSE, the x-axis will be removed (ticks, x-axis labels and title).
x_axis_title	Optional. Default NULL If present, will be the x-axis title. Else defaults to the provided x_coords
y_axis	Optional. Default TRUE If FALSE, the y-axis will be removed (ticks, y-axis labels and title).
y_axis_title	Optional. Default NULL If present, will be the y-axis title. Else defaults to the provided y_coords
title	Optional. Default NULL If present, will be the plot title. Else defaults to the provided x_coords vs y_coords
legend_title	Optional. Default NULL If present will be the title of the legend. Else defaults to "Signal".
return_object	Optional. Default FALSE If present the ggplot object will be returned
x_axis_num_breaks	Optional. Default 5 Number of ticks on the x axis
y_axis_num_breaks	Optional. Default 5 Number of ticks on the y axis
palette	Required. Default NULL One of the RColorbrewer or viridis colour palettes
col_direction	Optional. Default 1 If -1, the colour scale will be reversed.
extrapolate_on	Optional. Default NULL If present, colours from the palette will be extrapolated between lightest and darkest to create the gradient. This value cannot be more than 100.
x_axis_text_size	Optional. Default 10 x-axis text size
y_axis_text_size	Optional. Default 10 y-axis text size
text_size	Optional. Default 10 text size of text elements in the plot.
legend_title_text_size	Optional. Default 8 text size of the legend title
legend_text_size	Optional. Default 8 text size of the legend text
title_size	Optional. Default 10 text size of the title
tad_ranges	Optional. Default NULL A GenomicRanges object specifying the start and end coordinates of TADs to be plotted on the heatmap.
group_col	Optional. Default NULL Name of the column which will be used to categorize TADs as belonging to either the first or the second Brick stores. This must be a numeric value ranging from 1 to 2. If NULL, TADs will be plotted on both Hi-C maps.
tad_colour_col	Optional. Default NULL tad_colour_col takes as value the column name in the tad_ranges object corresponding to the column which should be used to define different TAD categories.
colours	Optional. Default NULL If tad_ranges is present, colours expects a hexcode value of length 1. But, if tad_colour_col is specified, it expects colours of the same length as unique tad_ranges$tad_colour_col.
colours_names	Optional. Default NULL If present, will be assigned to colours. Else, will inherit unique tad_colour_col. If tad_colour_col is also absent, will revert to a placehold column name.
cut_corners	Optional. Default FALSE if cut_corners is TRUE, TAD borders will not be truncated, and they will span until the end of visible heatmap.
highlight_points	Optional. Not yet implemented.
width	Optional. Default 10cm Width of the output file units.
height	Optional. Default 6cm Height of the output file in units.
line_width	Optional. Default 0.5 When plotting TADs set the width of the plotted lines
units	Optional. Default cm Defines the units of the output file width and height.
legend_key_width	Optional. Default unit(3,"cm") Defines the legend key width.
legend_key_height	Optional. Default unit(0.5,"cm") Defines the legend key height.

Details

This function provides the capability to plot various types of heatmaps from Hi-C data.

• One sample heatmap.

• Two sample heatmap (One sample on upper and other on lower).

• All of the above with 90 degree rotation.

• All of the above but with signal capped at a certain value.

• All of the above but filtered by distance.

• All of the above with TADs/TAD borders plotted on top.

Value

If return_object is set to TRUE, the constructed ggplot2 object will be returned. Else TRUE.

Examples

FailSafe_log10 <- function(x){
     x[is.na(x) | is.nan(x) | is.infinite(x)] <- 0
     return(log10(x+1))
}

Bintable.path <- system.file(file.path("extdata", "Bintable_100kb.bins"), 
package = "HiCBricks")

out_dir <- file.path(tempdir(), "vizart_test")
dir.create(out_dir)

My_BrickContainer <- Create_many_Bricks(BinTable = Bintable.path, 
    bin_delim = " ", output_directory = out_dir, file_prefix = "Test",
    experiment_name = "Vignette Test", resolution = 100000,
    remove_existing = TRUE)

Matrix_file <- system.file(file.path("extdata", 
"Sexton2012_yaffetanay_CisTrans_100000_corrected_chr3R.txt.gz"), 
package = "HiCBricks")

Brick_load_matrix(Brick = My_BrickContainer, chr1 = "chr3R", 
chr2 = "chr3R", matrix_file = Matrix_file, delim = " ",
remove_prior = TRUE, resolution = 100000)

Brick_vizart_plot_heatmap(File = "./chr3R-1-10000000.pdf", 
Bricks = list(My_BrickContainer), resolution = 100000, 
x_coords = "chr3R:1:10000000", palette = "Reds", 
y_coords = "chr3R:1:10000000", FUN = FailSafe_log10, 
value_cap = 0.99, width = 10, height = 11, legend_key_width = unit(3,"mm"),
legend_key_height = unit(0.3,"cm"))

koustav-pal/HiCBricks documentation built on Oct. 25, 2022, 12:06 a.m.