trellis_rainfall_plot {YAPSA} | R Documentation

## Create a rainfall plot in a trellis structure

### 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"))

[Package YAPSA version 1.16.0 Index]