Show Copy Number Components

Show classified components ("Wang" ("W") method) for copy number data.

show_cn_components(
  parameters,
  method = "Wang",
  show_weights = TRUE,
  log_y = FALSE,
  return_plotlist = FALSE,
  base_size = 12,
  nrow = 2,
  align = "hv",
  ...
)

Arguments

parameters

a data.frame contain parameter components, obtain this from sig_tally function.

method

method for feature classification, can be one of "Wang" ("W"), "S" (for method described in Steele et al. 2019), "X" (for method described in Tao et al. 2023).

show_weights

default is TRUE, show weights for each component. Only used when method is "Macintyre".

log_y

logical, if TRUE, show log10 based y axis, only works for input from "Wang" ("W") method.

return_plotlist

if TRUE, return a list of ggplot objects but a combined plot.

base_size

overall font size.

nrow

(optional) Number of rows in the plot grid.

align

(optional) Specifies whether graphs in the grid should be horizontally ("h") or vertically ("v") aligned. Options are "none" (default), "hv" (align in both directions), "h", and "v".

...

other options pass to plot_grid function of cowplot package.

Value

a ggplot object

Author

Shixiang Wang w_shixiang@163.com