sapphire_plot: Sapphire plot - plotting annotation and progrex index
In CampaR1: Trajectory Analysis

Description Usage Arguments Details Value See Also Examples

View source: R/plot_zapphire.R

sapphire_plot is able to generate a sapphire plot using the progrex index file (e.g. "REPIX_000000000001.dat") generated by gen_annotation.

sapphire_plot(sap_file = NULL, sap_table = NULL, write = F,
  folderPlot = "plots/", timeline = T, local_cut = T, ann_trace = F,
  ann_trace_ret = F, background_height = NULL, ann_names_L = NULL,
  ann_names_R = NULL, title = "no title")

`sap_file`	Annotated progrex index file. This can be left unused if `sap_table` is used instead. This input must be the file output of `gen_annotation`.
`sap_table`	Annotated progrex index table. As for `sap_file` it can be left unused if the other input is used. Also in this case the format of the table must be the file output of `gen_annotation`.
`write`	A logical indicating whether to write the plot to file.
`folderPlot`	A character string that defines the folder in which save the plots (`write` argument must be `TRUE`).
`timeline`	A logical indicating whether add a timeline annotation (with the original order) on the bottom of the plot.
`local_cut`	A logical that, if `TRUE` plots the local cut annotation function (see `gen_annotation`).
`ann_trace`	This argument can be set to logical, an integer or a matrix of integers. If logical, the annotation will be a horizontal thick line that follows a split in half of the original timeline. If only an integer have been inserted the time line will be split in that number of splits. Instead if a matrix have been inserted it will be a plotted as it is on the top of the plot mapping the range of numbers in order to produce a gray scale horizontal annotation.
`ann_trace_ret`	If `TRUE` the annotation vector is returned.
`background_height`	Defines the height on which to put the annotation (integer between 1 and 14).
`ann_names_L`	Vector of characther strings indicating, from top on the left, the names of the annotation horizontal bars.
`ann_names_R`	Vector of characther strings indicating, from top on the right, the names of the annotation horizontal bars.
`title`	Title of the plot

For details, please refer to the main documentation of the original campari software http://campari.sourceforge.net/documentation.html.

If ann_trace_ret is active it will return the annotation trace used for the plot.

mst_from_trj, gen_progindex, gen_annotation.

adjl <- mst_from_trj(trj = matrix(rnorm(1000), nrow = 100, ncol = 10))
ret<-gen_progindex(adjl = adjl)
gen_annotation(ret_data = ret, local_cut_width = 10)
## Not run: 
zap_ggplot("REPIX_000000000001.dat")

## End(Not run)