Description Usage Arguments Value Examples
Heat map of the distance of the given relative copy numbers to whole numbers after scaling to absolute copy numbers for various ploidies and cellularities.
1 2 3 4 5 6 7 8 9 10 11 | absolute_copy_number_distance_heatmap(
relative_copy_numbers,
weights = NULL,
distance_function = "MAD",
min_ploidy = 1.5,
max_ploidy = 5.5,
low_distance_colour = "red",
high_distance_colour = "blue",
xlabel = "cellularity",
ylabel = "ploidy"
)
|
relative_copy_numbers |
a numeric vector containing relative copy numbers, i.e. ratios of copy numbers to the average copy number. |
weights |
a numeric vector of weights to apply to each copy number value (should be same length as relative_copy_numbers) |
distance_function |
the distance function to use, either "MAD" for the mean absolute difference or "RMSD" for the root mean square difference, where differences are between the fitted absolute copy number values and the nearest whole number. |
min_ploidy |
the minimum ploidy to display. |
max_ploidy |
the minimum ploidy to display. |
low_distance_colour |
the colour for low distances. |
high_distance_colour |
the colour for high distances. |
xlabel, ylabel |
x- and y-axis labels. |
a ggplot
object
1 2 3 4 5 6 7 8 9 | data(copy_number)
copy_number <- copy_number[copy_number$sample == "X17222", ]
segments <- copy_number_segments(copy_number)
absolute_copy_number_distance_heatmap(
segments$copy_number,
segments$weight,
distance_function = "MAD"
)
|
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