plot_genes_branched_pseudotime: Plot the branch genes in pseduotime with separate branch...

In cole-trapnell-lab/monocle-release: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

Works similarly to plot_genes_in_psuedotime esceptit shows one kinetic trend for each lineage.

Usage

plot_genes_branched_pseudotime(cds, branch_states = NULL, branch_point = 1,
  branch_labels = NULL, method = "fitting", min_expr = NULL,
  cell_size = 0.75, nrow = NULL, ncol = 1, panel_order = NULL,
  color_by = "State", expression_curve_linetype_by = "Branch",
  trend_formula = "~ sm.ns(Pseudotime, df=3) * Branch",
  reducedModelFormulaStr = NULL, label_by_short_name = TRUE,
  relative_expr = TRUE, ...)

Arguments

cds	CellDataSet for the experiment
branch_states	The states for two branching branchs
branch_point	The ID of the branch point to analyze. Can only be used when reduceDimension is called with method = "DDRTree".
branch_labels	The names for each branching branch
method	The method to draw the curve for the gene expression branching pattern, either loess ('loess') or VGLM fitting ('fitting')
min_expr	The minimum (untransformed) expression level to use in plotted the genes.
cell_size	The size (in points) of each cell used in the plot
nrow	Number of columns used to layout the faceted cluster panels
ncol	Number of columns used to layout the faceted cluster panels
panel_order	The a character vector of gene short names (or IDs, if that's what you're using), specifying order in which genes should be layed out (left-to-right, top-to-bottom)
color_by	The cell attribute (e.g. the column of pData(cds)) to be used to color each cell
expression_curve_linetype_by	The cell attribute (e.g. the column of pData(cds)) to be used for the linetype of each branch curve
trend_formula	The model formula to be used for fitting the expression trend over pseudotime
reducedModelFormulaStr	A formula specifying a null model. If used, the plot shows a p value from the likelihood ratio test that uses trend_formula as the full model
label_by_short_name	Whether to label figure panels by gene_short_name (TRUE) or feature id (FALSE)
relative_expr	Whether or not the plot should use relative expression values (only relevant for CellDataSets using transcript counts)
...	Additional arguments passed on to branchTest. Only used when reducedModelFormulaStr is not NULL.

Details

This plotting function is used to make the branching plots for a branch dependent gene goes through the progenitor state and bifurcating into two distinct branchs (Similar to the pitch-fork bifurcation in dynamic systems). In order to make the bifurcation plot, we first duplicated the progenitor states and by default stretch each branch into maturation level 0-100. Then we fit two nature spline curves for each branchs using VGAM package.

Value

a ggplot2 plot object

cole-trapnell-lab/monocle-release documentation built on May 13, 2019, 8:50 p.m.