Brick_vizart_plot_heatmap: Create the entire HDF5 structure and load the bintable
In HiCBricks: Framework for Storing and Accessing Hi-C Data Through HDF Files

Description Usage Arguments Details Value Examples

Brick_vizart_plot_heatmap creates various heatmaps and plots TADs.

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")
)

`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.

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.

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

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"))