Description Usage Arguments Details Value Examples

Visualization of differential TAD boundaries

1 2 3 |

`tad_diff` |
Raw object output by TADCompare. Required. |

`cont_mat1` |
contact matrix in either sparse 3 column, n x n or n x (n+3) form where the first three columns are coordinates in BED format. See "Input_Data" vignette for more information. If an x n matrix is used, the column names must correspond to the start point of the corresponding bin. Should correspond to the first contact matrix input into TADCompare. Required. |

`cont_mat2` |
contact matrix in either sparse 3 column, n x n or n x (n+3) form where the first three columns are coordinates in BED format. If an x n matrix is used, the column names must correspond to the start point of the corresponding bin. Should correspond to the second contact matrix input into TADCompare. Required. |

`resolution` |
Resolution of the data. Required. |

`start_coord` |
The start coordinate defining a region to plot. Required. |

`end_coord` |
The end coordinate defining a region to plot. Required. |

`pre_tad` |
A list of pre-defined TADs for drawing. Must contain two entries with the first corresponding to TADs detected in matrix 1 and the second to those detected in matrix 2. Each entry must contain a BED-like data frame or GenomicRanges object with columns "chr", "start", and "end", corresponding to coordinates of TADs. Must correspond to TADCompare results obtained for the same pre-defined TADs. Optional |

`show_types` |
If FALSE only the labels "Differential" and "Non-Differential" will be used. More in-depth differential boundary types will be excluded. Default is TRUE. |

`point_size` |
Parameter used to adjust the size of boundary points on heatmap plot. Default is 3. |

`max_height` |
Maximum height in bins that should be displayed on the heatmap plot. Default is 25. |

`rel_heights` |
Proportion of the size of the heatmap and score panels. Should be a vector containing the relative size of each panel with the heatmap panel coming first and the score panel second. Default is c(2, 1). |

`palette` |
Parameter used to adjust color palette. For list of palettes see https://rdrr.io/cran/RColorBrewer/man/ColorBrewer.html. Alternatively, users can define a vector of color names or hex codes. Default is 'RdYlBu' |

Given a TADCompare object and two corresponding contact matrices, Diff_Plot provides visualization of user-specified regions of the genome with accompanying differential annotations, TAD scores and differential TAD scores

A ggplot plot containing a visualization of the upper diagonal both contact matrices with types of non-/differential boundaries labeled. The first matrix is shown on top and the second on the bottom. If pre_tad is provided, then the outline of the pre-defined TADs are shown. Individual TAD score and differential TAD scores are shown below the contact matrix plots.

1 2 3 4 5 6 7 8 | ```
# Read in data
data("rao_chr22_prim")
data("rao_chr22_rep")
# Find differential TAD boundaries
tad_diff <- TADCompare(rao_chr22_prim, rao_chr22_rep, resolution = 50000)
# Create plot
DiffPlot(tad_diff,rao_chr22_prim, rao_chr22_rep, resolution = 50000,
start_coord = 22050000, end_coord = 24150000)
``` |

TADCompare documentation built on Nov. 8, 2020, 6:48 p.m.

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