plotDANA: Scatter plot DANA assessment metrics

In LXQin/DANA: Data-driven Normalization Assessment for miRNA-Seq Data

Scatter plot DANA assessment metrics

Description

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.

LXQin/DANA documentation built on March 7, 2024, 3:24 a.m.