apl_coords: Calculate Association Plot coordinates

In elagralinska/APLpackage: Association Plots

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 standard 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}) := ≤ft|\vec{r}\right|\cos(φ(\vec{r}))

y(\vec{r}) := ≤ft|\vec{r}\right|\sin(φ(\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.

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)

elagralinska/APLpackage documentation built on Dec. 20, 2021, 4:15 a.m.