biplot_corral: Generate biplot for corral object

In laurenhsu1/corral: Correspondence Analysis for Single Cell Data

Generate biplot for corral object

Description

Generate biplot for corral object

Usage

biplot_corral(
  corral_obj,
  color_vec,
  text_vec,
  feat_name = "(genes)",
  nfeat = 20,
  xpc = 1,
  plot_title = "Biplot",
  text_size = 2,
  xjitter = 0.005,
  yjitter = 0.005,
  coords = c("svd", "PC", "SC")
)

Arguments

corral_obj	list outputted by the corral function
color_vec	vector; length should correspond to the number of rows in v of corral_obj, and each element of the vector classifies that cell (entry) in the embedding to that particular class, which will be colored the same. (e.g., cell type)
text_vec	vector; length should correspond to the number of rows in u of corral_obj, and each element of the vector is the label for the respective feature that would show on the biplot.
feat_name	char; the label will in the legend. Defaults to (genes).
nfeat	int; the number of features to include. The function will first order them by distance from origin in the selected dimensions, then select the top n to be displayed.
xpc	int; which PC to put on the x-axis (defaults to 1)
plot_title	char; title of plot (defaults to *Biplot*)
text_size	numeric; size of the feature labels given in text_vec (defaults to 2; for ggplot2)
xjitter	numeric; the amount of jitter for the text labels in x direction (defaults to .005; for ggplot2)
yjitter	numeric; the amount of jitter for the text labels in y direction (defaults to .005; for ggplot2)
coords	char; indicator for sets of coordinates to use. svd plots the left and right singular vectors as outputted by SVD (u and v), which PC and SC use the principal and standard coordinates, respectively (defaults to svd)

Value

ggplot2 object of the biplot

Examples

library(DuoClustering2018)
library(SingleCellExperiment)
zm4eq.sce <- sce_full_Zhengmix4eq()
zm4eq.countmat <- counts(zm4eq.sce)
zm4eq.corral_obj <- corral(zm4eq.countmat)
gene_names <- rowData(zm4eq.sce)$symbol
ctvec <- zm4eq.sce$phenoid

biplot_corral(corral_obj = zm4eq.corral_obj, color_vec = ctvec, text_vec = gene_names)

laurenhsu1/corral documentation built on Feb. 19, 2023, 10:37 p.m.