plot_dims: Plot reduced dimensions

Description Usage Arguments Value

View source: R/plot_dims.R

Description

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

Usage

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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.