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

Description Usage Arguments Details Value

Description

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

Usage

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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


monocle documentation built on Nov. 8, 2020, 5:06 p.m.