plot_dims: Plot reduced dimensions

In campsj/scTools: Tools to help with analysis of single-cell transcriptome datasets

Description

Plot reduced dimensions from singlecellexperiment object and var them on color or plot expression level

Usage

plot_dims(sce_object, x = "PC1", y = "PC2", color, shape = NA,
  labels = NA, col_values = NA, point_size = 3, alpha = 1,
  theme = 12, label_size = 18, nrow = NULL, ncol = NULL)

Arguments

sce_object	A single cell experiment object
x	Principal component to plot on x axis
y	Principal component to plot on y axis
color	factor for color
shape	factor for shape
labels	list containing labels for gene names
col_values	Manuel entry of colors or HEX color codes to plot
point_size	Size parameter of geom_point
alpha	Decide the transparency of geom
theme	numerical specifying base size of theme
label_size	numerical specifying size of facet titles ie genes
nrow	numerical specifying the amount of rows
ncol	numerical specifying the amount of columns

Value

Ggplot object plot of single-cell dataset with variables or genes as color scale

campsj/scTools documentation built on May 16, 2019, 11:10 p.m.