colocalization (version 1.0.2)

plot.colocal: Making scatter plots for signal proportions before and after d-type or z-type normalization

Description

This function is used to make scatter plots for signal proportions based on the results returned from the nsinc.d or nsinc.z function.

Usage

# S3 method for colocal
plot(x, …)

Arguments

x

an object of class "colocal", containing the results returned from nsinc.d or nsinc.z.

…

further arguments to be passed from or to other methods.

Value

plot.colocal returns a list of plots which summarize the results returned from the nsinc.d or nsinc.z function.

Details

The function currently works for results from nsinc.d or nsinc.z with bi-direction colocalization for dual-color images. At each proximity size r, the function makes two panels of scatter plots for signal proportions at all signals before and after d-type or z-type normalizations. Each signal in the original image contributes a point in the scatter plots whose x coordinate is the proportion of signals in one channel and y coordinate is the other channel. The scatter plots have the same color codes as signals in the original image. If the returned results contain colocalization results at multiple r's, then the scatter plots at each r are generated.

References

Liu, X., Xu, J., Guy C., Romero E., Green D., Cheng, C., Zhang, H. (2019). Unbiased and Robust Analysis of Co-localization in Super-resolution Images. Manuscript submitted for publication.

Examples

# NOT RUN {
## a simulated 3D example data.
data("twolines")

twolines.results <- nsinc.d(data = twolines, membership = "membership",
                            dim = 3, r.model = "r.med")

##plot(twolines.results)
# }