# apl_coords: Calculate Association Plot coordinates In ClemensKohl/APL: Association Plots

 apl_coords R Documentation

## Calculate Association Plot coordinates

### Description

Calculates the Association Plot coordinates for either the rows, columns or both (default).

### Usage

apl_coords(caobj, group, calc_rows = TRUE, calc_cols = TRUE)


### Arguments

 caobj A "cacomp" object with principal row coordinates and standardized column coordinates calculated. group Numeric/Character. Vector of indices or column names of the columns to calculate centroid/x-axis direction. calc_rows TRUE/FALSE. Whether apl row coordinates should be calculated. Default TRUE. calc_cols TRUE/FALSE. Whether apl column coordinates should be calculated. Default TRUE.

### Details

Coordinates (x,y) of row vector \vec{r} are defined as

x(\vec{r}) := \left|\vec{r}\right|\cos(\phi(\vec{r}))

y(\vec{r}) := \left|\vec{r}\right|\sin(\phi(\vec{r}))

The x-direction is determined by calculating the centroid of the columns selected with the indices in "group".

### Value

Returns input "cacomp" object and adds components "apl_rows" and/or "apl_cols" for row and column coordinates. In "group" the indices of the columns used to calculate the centroid are saved.

### References

Association Plots: Visualizing associations in high-dimensional correspondence analysis biplots Elzbieta Gralinska, Martin Vingron bioRxiv 2020.10.23.352096; doi: https://doi.org/10.1101/2020.10.23.352096

### Examples

set.seed(1234)
# Simulate scRNAseq data
cnts <- data.frame(cell_1 = rpois(10, 5),
cell_2 = rpois(10, 10),
cell_3 = rpois(10, 20),
cell_4 = rpois(10, 20))
rownames(cnts) <- paste0("gene_", 1:10)
cnts <- as.matrix(cnts)

# Run correspondence analysis
ca <- cacomp(obj = cnts, princ_coords = 3)
# Calculate APL coordinates
ca <- apl_coords(ca, group = 3:4)


ClemensKohl/APL documentation built on Feb. 6, 2024, 1:28 a.m.