trellis_rainfall_plot: Create a rainfall plot in a trellis structure

In YAPSA: Yet Another Package for Signature Analysis

Description

A trellis is a plot structure which allows space optimized multi-panel multi track plots. This function uses the package gtrellis developed by Zuguang Gu, also available at http://www.bioconductor.org/packages/release/bioc/html/gtrellis.html. The graphics in the tracks within a gtrellis plot are mostly drawn with functions from the package grid. Note that for technical reasons, the column indicating the chromosome MUST have the name chr and be the first column in the data frame supplied to the gtrellis functions. Therefore reformatting is performed in this function before calling gtrellis functions.

Usage

trellis_rainfall_plot(
  in_rainfall_dat,
  in_point_size = unit(1, "mm"),
  in_rect_list = NULL,
  in_title = "",
  in_CHROM.field = "CHROM",
  in_POS.field = "POS",
  in_dist.field = "dist",
  in_col.field = "col"
)

Arguments

in_rainfall_dat	Data frame which has to contain at least columns for chromosome, position, intermutational distance and colour information
in_point_size	size of the points in the rainfall plot to be created has to be provided with appropriate units, e.g. in_point_size=unit(0.5,"mm")
in_rect_list	Optional argument, if present, will lead to highlighting of specified regions by coloured but transparent rectangles
in_title	Title in the figure to be created.
in_CHROM.field	String indicating which column of in_rainfall_dat carries the chromosome information
in_POS.field	String indicating which column of in_rainfall_dat carries the position information
in_dist.field	String indicating which column of in_rainfall_dat carries the intermutational distance information
in_col.field	String indicating which column of in_rainfall_dat carries the colour information encoding the nucleotide exchange

Value

The function doesn't return any value.

The function doesn't return any value.

See Also

gtrellis_layout

add_track

grid.points

Examples

 data(lymphoma_test)
 choice_PID <- "4121361"
 PID_df <- subset(lymphoma_test_df,PID==choice_PID)
 trellis_rainfall_plot(PID_df,in_point_size=unit(0.5,"mm"))

YAPSA documentation built on Nov. 8, 2020, 4:59 p.m.