Scatter plot DANA assessment metrics

Plot function for a scatter plot of the DANA result metrics generated using the DANA normalization assessment assessNormalization. The DANA Assessment metrics for given normalized counts (for each normalized count matrix) are provided as a data.frame with the columns:

cc: cc measures the preservation of biological signals before versus after normalization. A high value indicates a high preservation of biological signals (cc <= 1)
mscr: mscr measures the relative reduction of handling before versus after normalization. A high mscr indicates higher removal of handling effects.

When selecting a normalization method for the raw data, one should aim for the best possible trade-off of hight cc and high mscr. This function generates a ggplot scatter plot of the DANA metrics for the selection of a most suitable normalization method.

Usage

plotDANA(
  metrics,
  label.size = 3,
  label.repel = TRUE,
  limits.x,
  limits.y,
  title
)

Arguments

metrics: data.frame of DANA metrics containing the metrics cc and mscr as columns. Each row represents a normalization method.
label.size: Optional. Text size of the plot labels.
label.repel: Optional. Logical if the ggrepel package is used to space point labels. Requires the package ggrepel to be installed.
limits.x: Optional. Must be either missing, NA, or c(x1,x2). If not given, x-axis limits are set to [0,1]. If NA, x-axis limits are automatically scaled to the data. If c(x1,x2), x-axis limits are scaled to the interval [x1,x2].
limits.y: Optional. Must be either missing, NA, or c(y1,y2). If not given, y-axis limits are set to [0,1]. If NA, y-axis limits are automatically scaled to the data. If c(y1,y2), y-axis limits are scaled to the interval [y1,y2].
title: Optional. Plot title

Value

ggplot2 object of a scatter plot for the given DANA metrics.