BoxScatter_Plot: Function to make Box-Scatter plots.

In davidrequena/drfun: Functions To Help With RNAseq Data Analysis

Function to make Box-Scatter plots.

Description

This function will make a Boxplot, using a DEseq object. It will show the data points on top with a small deviation (jitter) for a better visualization.

Usage

BoxScatter_Plot(
  object = NULL,
  variables = c(fill = "VarFill", shape = "VarShape"),
  genename = NULL,
  symbol = NULL,
  labels = c("N", "P", "R", "M"),
  categories = c("normal", "primary", "recurrence", "metastasis"),
  colors = NULL,
  shapes = NULL,
  markersize = NULL,
  alpha = 0.8,
  width = NULL,
  height = NULL,
  jitter = 0.2,
  dpi = 150,
  save = FALSE,
  title_size = c(axis = 20, fig = 24),
  label_size = c(x = 20, y = 16),
  legend_size = c(title = 14, elements = 12)
)

Arguments

object	A DEseq object already transformed with the variance stabilizing or rlog transformations.
variables	To indicate the variables to be used as Shape and Fill of the markers.
genename	The gene name to be used for the plot.
symbol	The gene symbol to be used for the plot.
labels	A vector containing the x-labels of the box-plot. Default: c("N", "P", "R", "M").
categories	A vector containing the labels for the legend. Default: c("normal", "primary", "recurrence", "metastasis").
colors	Vector of colors to be used for the categories of the variable assigned as Marker Fill.
shapes	Vector of shapes to be used for the categories of the variable assigned as Marker Shape.
markersize	Size of the marker.
alpha	Transparency of the marker, which goes from 0 (transparent) to 1 (no transparent). Default: 0.8.
width	Width of the plot.
height	Height of the plot.
jitter	Random deviation added to the dots. Default: 0.2.
dpi	DPI of the plot. Default: 150.
save	To save the plot. Default: FALSE.
title_size	Font of the title and axis names. Default: c(axis = 20, fig = 24).
label_size	Font of the labels (x-axis) and numbers (y-axis). Default: c(x = 20, y = 16).
legend_size	Font of the title and elements of the legend. Default: c(title = 14, elements = 12).

davidrequena/drfun documentation built on May 15, 2024, 10:33 a.m.