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Plot PCA embedding of the 3 big cohorts to serve as a base plot

Source: R/get_base_plot.R
get_base_plot.Rd

Plot PCA embedding of the 3 big cohorts to serve as a base plot

Usage

get_base_plot(
  x = "PC3",
  y = "PC4",
  color = "pam50",
  size_dots = 2,
  alpha_val = 0.1,
  size_legend = 4,
  base_size = 10
)

Arguments

x

A string. PC for x-axis

y

A string. PC for y-axis

color

A string. Which column to use when coloring the dots.

size_dots

An integer. Size of the points in the plot

alpha_val

A number. Alpha value of the points

size_legend

An integer. Size of the color legend

base_size

An integer. Parameter for ggplot2::theme_bw

Value

A plot of the TCGA, SCANB and METABRIC embedding