plotScatter: Gene Expression Scatterplot

In farrellja/URD: URD

Description

Gene Expression Scatterplot

Usage

plotScatter(
  object,
  label.x,
  label.y,
  label.color = NULL,
  label.x.type = "search",
  label.y.type = "search",
  label.color.type = "search",
  cells = NULL,
  point.size = 1,
  point.alpha = 1,
  xlim = NULL,
  ylim = NULL,
  density.background = T,
  density.color = "#888888",
  density.bandwidth = 1,
  density.bins = 128,
  density.exclude.origin = T,
  xlab = label.x,
  ylab = label.y,
  colorlab = label.color,
  title = "",
  legend = T
)

Arguments

object	An URD object
label.x	(Character) Value to plot on the x-axis
label.y	(Character) Value to plot on the y-axis
label.color	(Character) Value to plot as point color
label.x.type	(Character) Where to look for the label.x; Default is "search" which looks in order: "meta", "group", "sig", "gene", "pseudotime", "pc", "diff.data"
label.y.type	(Character) Where to look for the label.y; Default is "search" which looks in order: "meta", "group", "sig", "gene", "pseudotime", "pc", "diff.data"
label.color.type	(Character) Where to look for the label.color; Default is "search" which looks in order: "meta", "group", "sig", "gene", "pseudotime", "pc", "diff.data"
cells	(Character vector) Names of cells to include in the plot (Default, NULL is all cells.)
point.size	(Numeric) Adjust size of points on the plot
point.alpha	(Numeric) Adjust transparency of points on the plot
xlim	(Numeric vector) X-axis limits (Default NULL lets ggplot2 automatically decide.)
ylim	(Numeric vector) Y-axis limits (Default NULL lets ggplot2 automatically decide.)
density.background	(Logical) Should
density.color	(Character) Darkest color of the density scale
density.bandwidth	(Numeric) The kernel bandwidth used in calculating the density background is multiplied by this factor.
density.bins	(Numeric) Number of bins to use for 2D kernel estimation.
density.exclude.origin	(Logical) Whether values with expression (0,0) should be excluded from the density calculation. (The number of non-expressing cells can often overwhelm the density calculation and make it useless if the genes plotted are specific to a particular lineage and cells is not used to restrict the cells on the plot.)
xlab	(Character) X-axis label
ylab	(Character) Y-axis label
colorlab	(Character) Color guide label
title	(Character) Title of plot
legend	(Logical) Display a legend

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.