Add Contact Map to Coverage Plot.

Add Contact Map to Coverage Plot.

geom_tad(
  matrix,
  granges,
  color.palette = NULL,
  value.cut = NULL,
  transform.fun = NULL,
  plot.space = 0.1,
  plot.height = 1,
  top = TRUE,
  show.rect = FALSE
)

Arguments

matrix

Matrix (n x n) contains contact map information.
granges

The rownames and colnames information of matrix.
color.palette

One of the RColorbrewer or viridis colour palettes. Parameter of Brick_vizart_plot_heatmap. Default: NULL.
value.cut

If present, values beyond a certain quantile will be capped to that quantile. Parameter of Brick_vizart_plot_heatmap. Default: NULL.
transform.fun

If any sort of transformations should be applied to the data before plotting. Parameter of Brick_vizart_plot_heatmap. Default: NULL.
plot.space

Top and bottom margin. Default: 0.1.
plot.height

The relative height of contact map to coverage plot. Default: 1.
top

Logical value, whether to place this plot on the coverage plot. Default: TRUE.
show.rect

Logical value, whether to add rect border to the plot. Default: FALSE.

Value

Plot.