calILRs: Calculate the Instantaneous Log Ratio between two branches

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

This function is used to calculate the Instant Log Ratio between two branches which can be used to prepare the heatmap demonstrating the branch gene expression divergence hirearchy. If "stretch" is specifified, each branch will be firstly stretched into maturation level from 0-100. Since the results when we use "stretching" are always better and IRLs for non-stretched spline curves are often mismatched, we may only turn down "non-stretch" functionality in future versions. Then, we fit two separate nature spline curves for each individual linages. The log-ratios of the value on each spline curve corresponding to each branch are calculated, which can be used as a measure for the magnitude of divergence between two branching branchs.

Usage

calILRs(cds, trend_formula = "~sm.ns(Pseudotime, df = 3)*Branch",
  branch_point = 1, trajectory_states = NULL, relative_expr = TRUE,
  stretch = TRUE, cores = 1, ILRs_limit = 3, label_by_short_name = TRUE,
  useVST = FALSE, round_exprs = FALSE, output_type = "all",
  branch_labels = NULL, file = NULL, return_all = F, verbose = FALSE,
  ...)

Arguments

cds	CellDataSet for the experiment
trend_formula	trend_formula a formula string specifying the full model in differential expression tests (i.e. likelihood ratio tests) for each gene/feature.
branch_point	the point where two branches diverge
trajectory_states	states corresponding to two branches
relative_expr	A logic flag to determine whether or not the relative expressed should be used when we fitting the spline curves
stretch	a logic flag to determine whether or not each branch should be stretched
cores	Number of cores when fitting the spline curves
ILRs_limit	the minimum Instant Log Ratio used to make the heatmap plot
label_by_short_name	label the rows of the returned matrix by gene_short_name (TRUE) or feature id (FALSE)
useVST	A logic flag to determine whether or not the Variance Stablization Transformation should be used to stablize the gene expression. When VST is used, the difference between two branchs are used instead of the log-ratio.
round_exprs	A logic flag to determine whether or not the expression value should be rounded into integer
output_type	A character either of "all" or "after_bifurcation". If "after_bifurcation" is used, only the time points after the bifurcation point will be selected
branch_labels	the name for each branch, for example, AT1 or AT2
file	the name for storing the data. Since the calculation of the Instant Log Ratio is very time consuming, so by default the result will be stored
return_all	A logic flag to determine whether or not all the results from the analysis should be returned, this includes a dataframe for the log fold change, normalized log fold change, raw divergence, normalized divergence, fitting curves for each branch
verbose	Whether or not detailed running information should be returned
...	Additional arguments passed to buildBranchCellDataSet

Value

a ggplot2 plot object

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