plot_multiple_branches_pseudotime {monocle} | R Documentation

## Create a kinetic curves to demonstrate the bifurcation of gene expression along multiple branches

### Description

Create a kinetic curves to demonstrate the bifurcation of gene expression along multiple branches

### Usage

    plot_multiple_branches_pseudotime(cds, branches, branches_name = NULL,
      min_expr = NULL, cell_size = 0.75, norm_method = c("vstExprs", "log"),
      nrow = NULL, ncol = 1, panel_order = NULL, color_by = "Branch",
      trend_formula = "~sm.ns(Pseudotime, df=3)", label_by_short_name = TRUE,
      TPM = FALSE, cores = 1)

### Arguments

`cds` | CellDataSet for the experiment (normally only the branching genes detected with BEAM)
`branches` | The terminal branches (states) on the developmental tree you want to investigate.
`branches_name` | Name (for example, cell type) of branches you believe the cells on the branches are associated with.
`min_expr` | The minimum level of expression to show in the plot
`cell_size` | A number how large the cells should be in the plot
`norm_method` | Determines how to transform expression values prior to rendering
`nrow` | the number of rows used when laying out the panels for each gene's expression
`ncol` | the number of columns used when laying out the panels for each gene's expression
`panel_order` | the 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
`trend_formula` | the model formula to be used for fitting the expression trend over pseudotime
`label_by_short_name` | label figure panels by gene_short_name (TRUE) or feature id (FALSE)
`TPM` | Whether to convert the expression value into TPM values.
`cores` | Number of cores to use when smoothing the expression curves shown in the heatmap.

### Value

a ggplot2 plot object

[Package monocle version 2.14.0 Index]