pseudotimePlotByGenes: pseudotimeplotByGenes

In Zouter/MPath: Mpath: a single-cell RNAseq data analysis algorithm that maps multi-branching single-cell trajectories revealing cell progression during development

Description

pseudotimeplotByGenes

Usage

pseudotimePlotByGenes(exprs, if_log2 = TRUE, cell_annotation, cell_order,
  plot_genes = NULL, reverse_order = FALSE, min_expr = -3,
  cell_size = 2, plot_cols = NULL,
  trend_formula = "expression ~ sm.ns(Pseudotime, df=3)")

Arguments

exprs	a data frame or matrix of log transformed expression data, with row of cells and column of genes
if_log2	whether exprs is log2 transformed
cell_annotation	a two column data frame of matrix annotating cells(cell ID or name) with cell types
cell_order	a vector stroing the order of cells with cell ID or name, same as appeared in row names of exprs
plot_genes	a vector storing the genes selected for plot, same as appeared in the column names of exprs, if NULL, all genes in exprs will be selected
reverse_order	reverse the order of the pseudotime
min_expr	the threshold for cutting of the cell expressions in regression values, values lower than this will be forced to min_exprs
cell_size	the size of cells in the plot
plot_cols	plot colours
trend_formula	the formula for regression analysis

Value

a object of ggplot

Examples

## Not run: 
pseudotimePlotByGenes(exprs = "FULL.log2TPM.txt", 
                      cell_annotation = "splAnnotation_outlierRemoved.txt", 
                      cell_order = "uspin.PCA.0.03.seed1.txt", 
                      plot_genes = "genes.txt", 
                      reverse_order = TRUE, plot_cols = 3)

## End(Not run)

Zouter/MPath documentation built on May 4, 2019, 2:31 p.m.