M3D_Plotting: Make M3Drop Plots

In tallulandrews/M3Drop: Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Make M3Drop Plots

Description

Background functions used for making M3Drop plots. Functions tagged with "bg__" are not meant for direct usage and are not available in the Bioconductor release.

Usage

	bg__dropout_plot_base(expr_mat, xlim=NA, suppress.plot=FALSE)
	bg__add_model_to_plot(fitted_model, base_plot, lty=1, lwd=1, col="dodgerblue", legend_loc="topright")
	bg__highlight_genes(base_plot, expr_mat, genes, col="darkorange", pch=16)

Arguments

expr_mat	a numeric matrix of normalized (not log-transformed) expression values, columns = samples, rows = genes.
xlim	limits of x-axis of plot, for comparing distributions across many datasets.
suppress.plot	Whether to make the plot or just return values.
fitted_model	output from fitting a model to dropout rate vs mean expression, see bg__fit_MM,bg__fit_ZIFA,bg__fit_logistic
base_plot	output from bg__dropout_plot_base
legend_loc	coordinates of top-right corner of the legend.
genes	list of genes to be highlighted.
col,lty,lwd,pch	Graphical parameters passed to plotted points & lines respectively.

Details

bg__dropout_plot_base plots grey-scale distribution of dropout-rate vs log10(mean expression) for each each. Colour indicates density of points light-grey = low, black = high.

bg__add_model_to_plot adds a line based on the predicted dropout rate for each gene from a particular model.

bg__highlight_genes highlights specified genes in the given colour.

Value

bg__dropout_plot_base A named list of output: p = dropout rate for each gene s = mean expression of each gene xes = log10 transformed mean expression of each gene data = original expression matrix order = ordering of xes from smallest to largest bg__add_model_to_plot Invisibly location of the plotted legend. bg__highlight_genes Invisibly the coordinates of the highlighted genes.

tallulandrews/M3Drop documentation built on March 6, 2024, 1:49 a.m.