Could it be possible to add copy-neutral LOH to the plot made using cnSpec?

[hoonghim]

Dear Zachary Skidmore,

hello, I'm trying to visualize copy number variation results for 36 cancer patients using GenVisR, cnSpec().

Thanks to your kind and easy-to-understand description, I could draw a plot for diverse copy-number variations.

This is an example part.

And I hope to add more information to this plot. I have information about copy-neutral loss of heterozygosity (LOH).

I made a data frame which includes copy-neutral loh information (chromosome, start, end, segmean, sample) For copy-neutral LOH, segmean is always 2. Thus, I would like to display the LOH area in yellow like this.

In Vignettes, I saw plotLayer option, which could utilize ggplot2.

Could you tell me how to display copy-neutral LOH on a plot?

Thank you for your reading and making this useful tool.

Sincerely,

Seung-hoon

[zlskidmore]

try something like this:

library(GenVisR)
library(ggplot2)
tmp <- data.frame("sample"=c("Luc1", "Luc1"), "chromosome"=c("5", "8"), "start"=c(20000000, 20000000), "end"=c(70000000, 70000000))
layer <- geom_rect(data=tmp, mapping=aes(xmin=start, xmax=end, ymin=0, ymax=1), fill="yellow", color="yellow")
cnSpec(LucCNseg, genome="hg19", plotLayer = layer)

[hoonghim]

Thank you so much for your help. It works very well!

And, could I give one more question?

I tried to make a legend which describes color information (Gain: Red, Loss: Blue, Copy-neutral LOH: Yellow) although there is already legend about copy number information like this.

The reason I try to make the legend is to inform people what yellow means.

I tried to do this by adding this code by referring to this question and answer https://stackoverflow.com/questions/23635662/editing-legend-text-labels-in-ggplot

###################### geom_rect(data=int.loh.cohort.df, mapping=aes(xmin=start, xmax=end, ymin=0, ymax=1, color="yellow"), fill="yellow") + scale_color_manual(labels = c("Gain", "Loss", "CN-LOH"), values = c("red", "blue", "yellow")) ####################### This gave me an error: Error: Cannot add ggproto objects together. Did you forget to add this object to a ggplot object? #######################

I don't know what the grammatical problem is.

Could you help me how to add color description?

Again, I sincerely appreciate your help.

Seung-hoon

[zlskidmore]

I think the problem is that you need to pass the ggplot items as a list to GenVisR, also you probably want scale_fill_manual()

On 12/23/18 9:21 AM, hoonghim wrote:

Thank you so much for your help. It works very well!

And, could I give one more question?

I tried to make a legend which describes color information (Gain: Red, Loss: Blue, Copy-neutral LOH: Yellow) although there is already legend about copy number information like this.

[image]https://user-images.githubusercontent.com/42195952/50384972-4d581480-0710-11e9-913a-35b8cb15fdb8.png

The reason I try to make the legend is to inform people what yellow means.

I tried to do this by adding this code by referring to this question and answer https://stackoverflow.com/questions/23635662/editing-legend-text-labels-in-ggplot

###################### geom_rect(data=int.loh.cohort.df, mapping=aes(xmin=start, xmax=end, ymin=0, ymax=1, color="yellow"), fill="yellow") + scale_color_manual(labels = c("Gain", "Loss", "CN-LOH"), values = c("red", "blue", "yellow")) ####################### This gave me an error: Error: Cannot add ggproto objects together. Did you forget to add this object to a ggplot object? #######################

I don't know what the grammatical problem is.

Could you help me how to add color description?

Again, I sincerely appreciate your help.

Seung-hoon

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