Copy Number feature request

[jessicadlang]

I have a use case for plotting HiC and other tracks alongside copy number information for a cancer dataset. It would be great to have code built for plotting log2 transformed copy number values (option to toggle on or off the log transformation depending on the data type), and plot with positive values and negative values in different colors. Additional features like changing the axis to be able to capture a copy-number appropriate range (i.e. so you can see single copy number loss or gain as well as major copy number loss or gain, and maybe representation as segments rather than a smoothed line.

Right now I hacked plotSignal() to plot positive and negative values separately and position them as if they are a single graph, but it's a little clunky and I can't add the additional features mentioned above. The CNA data.frame is essentially in bed format with the column "score" with log2 transformed CN.

plotSignal(
data = CNA,
chrom = "chrX",
range = c(0, 2),
baseline = FALSE,
negData = TRUE,
linecolor = "red",
fill = "red",
alpha = 0.8,
x = 0.25, y = 1, width = 3.5, height = 0.2,
)
plotSignal(
data = CNA,
chrom = "chrX",
range = c(-2, 0),
baseline = FALSE,
negData = TRUE,
linecolor = "blue",
fill = "blue",
alpha = 0.8,
x = 0.25, y = 1.2, width = 3.5, height = 0.2,
)

Very cool package!! Thanks for your time developing, maintaining, and sharing!

[nekramer]

Thanks for checking out plotgardener!! These are great suggestions, so I'm going to keep this issue open with the "enhancement" tag.

Just to note, and forgive me if I'm misunderstanding what you are plotting, but plotSignal can plot two datasets at once within the same plot. This can be useful to plot a negative dataset and positive dataset together. This also allows the option to color them differently. To do so, you would provide your datasets as a list to the data parameter and specify multiple colors in a vector to the linecolor and/or fill arguments. Also, it may help to use the range parameter to specify the y-axis range to capture more of a copy number-appropriate range. I hope this helps some of your plotting setbacks as we continue developing!

Best,
Nicole

[jessicadlang]

Thank you, I will check out these options on our data!