createFishObject: Create a fish object after doing some input validation and...

In chrisamiller/fishplot: Visualize the evolution of populations of cells over time

Create a fish object after doing some input validation and data munging

Description

Create a fish object after doing some input validation and data munging

Usage

createFishObject(
  frac.table,
  parents,
  timepoints = NULL,
  col = NULL,
  clone.labels = NULL,
  clone.annots = NULL,
  clone.annots.angle = 0,
  clone.annots.col = "black",
  clone.annots.pos = 2,
  clone.annots.cex = 0.7,
  clone.annots.offset = 0.2,
  fix.missing.clones = FALSE
)

Arguments

frac.table	A numeric matrix containing tumor fraction estimates for all clones at all timepoints
parents	An integer vector specifying parental relationships between clones
timepoints	An numeric vector specifying the timepoints for each column of the matrix
col	A vector of colors to use when plotting each clone
clone.labels	A character vector of names to assign to each clone when plotting a legend
clone.annots	A character vector of annotations (mutation) to label to each clone in the plot
clone.annots.angle	A numeric angle in degrees (0-360) giving the angle at which to plot the annotations
clone.annots.col	A string giving the color with which to draw the clone annotations
clone.annots.pos	An integer describing the position for the clone annotations (1=below, 2=left, 3=above, 4=right)
clone.annots.cex	A numeric specifying the clone annotation text size ("character expansion factor")
clone.annots.offset	A numeric specifying distance ("offset") of the annotation from the clone start point
fix.missing.clones	A boolean value, telling whether to "correct" clones that have zero values at timepoints between non-zero values. (the clone must still have been present if it came back). Default FALSE.

Value

A fish object with the relevant slots filled

Examples

timepoints=c(0,30,75,150)
frac.table = matrix(
    c(100, 45, 00, 00,
       02, 00, 00, 00,
       02, 00, 02, 01,
       98, 00, 95, 40),
    ncol=length(timepoints))
parents = c(0,1,1,3)
fish = createFishObject(frac.table,parents,timepoints=timepoints)

chrisamiller/fishplot documentation built on Sept. 15, 2023, 1:53 p.m.