plot.colocal: Making scatter plots for signal proportions before and after...

In colocalization: Normalized Spatial Intensity Correlation

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 class '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.

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.

Value

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

Author(s)

Xueyan Liu, Jiahui Xu, Cheng Cheng, Hui Zhang.

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

## a simulated 3D example data.
data("twolines")

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

##plot(twolines.results)

Example output

The method is 'nsinc.d'!
The input data has dimension of 3!
The input study region is 'NULL'!
The observed study region is [-0.994687642,0.991983793] X [-0.994783715,0.984829183] X [-0.25846953,0.343853326]!

 The default full r range for colocalization index of type d is [0.00550850564633427,2.03825393738339]!

The r.model = 'r.med'!
r.min = 0.722833786275035 is used!
r.max = 0.722833786275035 is used!
Because of r.min = r.max, r.count = 1 and r.adjust = 0 are used!
Bi-direction colocalization is considered!
index.d for r = 0.722833786275035 is -0.224788967716664 ;
The average coolocalization index of type d over all choosen r's is = -0.224788967716664!

colocalization documentation built on Oct. 23, 2020, 5:15 p.m.