createFishObject | R Documentation |
Create a fish object after doing some input validation and data munging
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
)
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. |
A fish object with the relevant slots filled
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)
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