plot_embedding: Plot selected PCs from an embedding

In laurenhsu1/corral: Correspondence Analysis for Single Cell Data

Plot selected PCs from an embedding

Description

Plot selected PCs from an embedding

Usage

plot_embedding(
  embedding,
  xpc = 1,
  ypc = xpc + 1,
  plot_title = paste0("Dim", xpc, " by Dim", ypc),
  color_vec = NULL,
  color_title = NULL,
  ellipse_vec = NULL,
  facet_vec = NULL,
  ptsize = 0.8,
  saveplot = FALSE,
  plotfn = paste(plot_title, xpc, sep = "_"),
  showplot = TRUE,
  returngg = FALSE,
  color_pal_vec = NULL,
  dimname = "Dim"
)

Arguments

embedding	matrix or other tabular format where columns correspond to PCs and rows correspond to cells (entries). corral and corralm objects are also accepted.
xpc	int; which PC to put on the x-axis (defaults to 1)
ypc	int; which PC to put on the y-axis (defaults to the one after xpc)
plot_title	char; title of plot (defaults to titling based on xpc and ypc)
color_vec	vector; length should correspond to the number of rows in embedding, 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., this could be indicating which batch each cell is from)
color_title	char; what attribute the colors represent
ellipse_vec	vector; length should correspond to the number of rows in embedding, and each element of the vector classifies that cell (entry) in the embedding to that particular class, and elements of the same class will be circled in an ellipse. (e.g., this could be indicating the cell type or cell line; works best for attributes intended to be compact)
facet_vec	vector; length should correspond to the number of rows in embedding, and each element of the vector classifies that cell (entry) in the embedding to that particular class. Plot will be faceted by this attribute.
ptsize	numeric; the size of the points as passed to geom_point(). Defaults to 0.8.
saveplot	boolean; whether or not to save the plot, defaults FALSE
plotfn	char; what the filename is to be called. (defaults to making a name based on plot_title and xpc)
showplot	boolean; whether or not to show the plot, defaults TRUE
returngg	boolean; whether or not to return a ggplot2 object, defaults FALSE
color_pal_vec	char; hex codes for the color palette to be used. Default is to use the ggthemes few for plots with less than 9 colors, and to use/"stretch" pals polychrome if more colors are needed.
dimname	char; the name of the dimensions. defaults to "Dim"

Value

default none; options to display plot (showplot), save plot (saveplot), and/or return ggplot2 object (returngg)

Examples

listofmats <- list(matrix(sample(seq(0,20,1),1000,replace = TRUE),nrow = 20),
                   matrix(sample(seq(0,20,1),1000,replace = TRUE),nrow = 20))
corralm_obj <- corralm(listofmats, ncomp = 5)
embed_mat <- corralm_obj$v
cell_type_vec <- sample(c('type1','type2','type3'),100,replace = TRUE)
plot_embedding(embedding = embed_mat, 
               xpc = 1, 
               plot_title = 'corralm plot',
               color_vec = cell_type_vec, 
               color_title = 'cell type',
               saveplot = FALSE)

# or, call directly on the corralm object              
plot_embedding(corralm_obj)

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