plot_pca: Plot PCA

In graeberlab/small.cell.project: small.cell.project

Description

Plots PCA from scores file (output of PCA_from_file)

Usage

plot_pca(file, info.name, info.type, title = "", labels = TRUE,
  label_file = NULL, label_name, PCx = "PC1", PCy = "PC2",
  ellipses = F, conf = 0.95, point_size = 3, savename = "example",
  saveplot = F, savetype = ".png", w = 8, h = 6, label_size = 3,
  colpalette = NULL, shape.palette = NULL, legendname = "default")

Arguments

file	File containing scores matrix
info.name	Vector of sample names
info.type	Vector of sample types in the same order
title	Title of the plot
labels	default=T, do you want labels
label_file	Separate file that has annotations you want to use for labeling. Samples should be in a column called "Score".
label_name	Name of column you want to use to label points in plot
PCx, PCy	PCs to display
ellipses	Construct confidence region based on groups in info.type, default = T
conf	default = 0.95
point_size	size of points
saveplot	do you want to save the plot
savetype	default=".pdf", ".png" is also possible
w	width default=8
h	height default=6
colpalette	a vector of colors that changes the default color scheme, default is NULL, e.g. something like c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
shape.palette	a vector of shapes that changes the default shapes, default is null, e.g. something like c(16,16,15,17,17,15,17)

graeberlab/small.cell.project documentation built on May 12, 2019, 5:16 p.m.