plot_genes_branched_pseudotime {monocle} | R Documentation

## Plot the branch genes in pseduotime with separate branch curves.

### 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

[Package monocle version 2.12.0 Index]