Brick_vizart_plot_heatmap {HiCBricks} | R Documentation

## 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"))

[Package HiCBricks version 1.4.0 Index]