plotDimReduceGrid: Mapping the dimensionality reduction plot

Description Usage Arguments Value Examples

View source: R/plot_dr.R

Description

Creates a scatterplot given two dimensions from a data dimensionality reduction tool (e.g tSNE) output.

Usage

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plotDimReduceGrid(dim1, dim2, matrix, size, xlab, ylab, color_low, color_mid,
  color_high, var_label)

Arguments

dim1

Numeric vector. First dimension from data dimensionality reduction output.

dim2

Numeric vector. Second dimension from data dimensionality reduction output.

matrix

Numeric matrix. Each row of the matrix will be plotted as a separate facet.

size

Numeric. Sets size of point on plot. Default 1.

xlab

Character vector. Label for the x-axis. Default 'Dimension_1'.

ylab

Character vector. Label for the y-axis. Default 'Dimension_2'.

color_low

Character. A color available from ‘colors()'. The color will be used to signify the lowest values on the scale. Default ’grey'.

color_mid

Character. A color available from 'colors()'. The color will be used to signify the midpoint on the scale.

color_high

Character. A color available from ‘colors()'. The color will be used to signify the highest values on the scale. Default ’blue'.

var_label

Character vector. Title for the color legend.

Value

The plot as a ggplot object

Examples

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celda.tsne <- celdaTsne(counts = celda.CG.sim$counts, celda.mod = celda.CG.mod)
plotDimReduceGrid(celda.tsne[,1], celda.tsne[,2], matrix = celda.CG.sim$counts, 
                  xlab = "Dimension1", ylab = "Dimension 2", var_label = "tsne", 
                  size = 1, color_low = "grey", color_mid = NULL, color_high = "blue")

compbiomed/celda documentation built on May 25, 2019, 3:58 a.m.