intensity2circle {peco} | R Documentation

## Infer angles for each single-cell samples using fluorescence intensities

### Description

We use FUCCI intensities to infer the position of the cells in cell cycle progression. The result is a vector of angles on a unit circle corresponding to the positions of the cells in cell cycle progression.

### Usage

    intensity2circle(mat, plot.it = FALSE, method = c("trig", "algebraic"))

### Arguments

`mat` | A matrix of two columns of summarized fluorescence intensity. Rows correspond to samples.
`plot.it` | TRUE or FALSE. Plot the fitted results.
`method` | The method used to fit the circle. `trig` uses trignometry to transform intensity measurements from cartesian coordinates to polar coordinates. `algebraic` uses an algebraic approach for circle fitting, using the conicfit package.

### Value

The inferred angles on unit circle based on the input intensity measurements.

### Author(s)

Joyce Hsiao

### Examples

    # use our data
    library(SingleCellExperiment)
    data(sce_top101genes)

    # FUCCI scores - log10 transformed sum of intensities that were
    # corrected for background noise
    ints <- colData(sce_top101genes)[,c("rfp.median.log10sum.adjust",
                              "gfp.median.log10sum.adjust")]
    intensity2circle(ints, plot.it=TRUE, method = "trig")

[Package peco version 1.6.0 Index]