plotDrGene: Create a scatterplot for each row of a normalized gene expression matrix where x and y axis are from a data dimensionality reduction tool.

Description

Create a scatterplot for each row of a normalized gene expression matrix where x and y axis are from a data dimensionality reduction tool.

Usage

plotDrGene(dim1, dim2, matrix, trim = c(-2, 2), rescale = TRUE, size = 1,
  xlab = "Dimension_1", ylab = "Dimension_2", color_low = "grey",
  color_mid = NULL, color_high = "blue")

Arguments

dim1

Numeric vector; first dimension from data dimensionality reduction output.

dim2

Numeric vector; second dimension from data dimensionality reduction output.

matrix

Counts matrix, will have cell name for column name and gene name for row name.

trim

A two element vector to specify the lower and upper cutoff for the data. Occurs after row scaling. Set to NULL to disable. Default c(-2,2).A two element vector to specify the lower and upper cutoff for the data. Occurs after normalization, log transformation, and row scaling. Set to NULL to disable. Default c(-2,2).

rescale

Boolean. If TRUE, will rescale counts matrix on a 0~1 scale. Default TRUE.

size

Numeic vector; size of point on plot. Default = 1.

xlab

Character vector, used as label for x axis. Default "Dimension_1".

ylab

Character vector, used as label for y axis. Default "Dimension_2".

color_low

Character vector of R colors available from the colors() function. The color will be used to signify the lowest values on the scale. Default: 'grey'

color_mid

Character vector of R colors available from the colors() function. The color will be used to signify the midpoint on the scale.

color_high

Character vector of R colors available from the colors() function. The color will be used to signify the highest values on the scale. Default: 'blue'