plotTenX: TenXSubset object data summaries

In yavorska/TenXAnalysisPackage: Analysis of the 10x Genomics 1.3 Million Cells Data

Description

A function that plots the data summaries with the quantities of interest defined by the user. See Details for the allowed combinations.

Usage

plotTenX(object, x, y, type, colorByCells = NULL, colorByGenes = NULL, ...)

Arguments

object	A TenXSubset object.
x	A character string indicating the values to appear on the x axis.
y	An optional character vector indicating the values to appear on the y axis.
type	An optional character string representing the type of figure to plot. This is one of histogram, density, boxplot, violin, or point. If this is left blank, the algorithm will output a list of suitable choices for the user to choose based on the x and y parameters.
colorByCells	An optional parameter specifying either: the indices of the cells to be coloured differently (end up with two distinct groups) "library" or "mouse" as a shortcut to colour based on existing groups
colorByGenes	An optional parameter specifying the numeric indices of the genes to be coloured differently.
...	Any additional parameters compatible with ggplot2.

Details

The basic idea of this function is to provide an each interface which allows one to visualise the data in different meaningful ways in order to locate inconsistencies or possible problems which may arise.

There are multiple combinations of parameters one can use, but obviously not all will work well together. As a result, the function provides the user with prompts:

• if necessary parameters are left out, the function suggests suitable values for these parameters

• if the parameters chosen are not compatible, the function suggests alternative parameter values based on the ones that have been chosen

Value

A ggplot2 object.

yavorska/TenXAnalysisPackage documentation built on May 29, 2019, 12:42 p.m.