CompareOnBranches: Compare feature values over different branches
In Albluca/ElPiGraph.R: Elastic principal graph construction

Compare feature values over different branches

CompareOnBranches(X, Paths, TargetPG, BootPG = NULL,
  OnlyIsomorphicBoot = TRUE, GroupsLab = NULL, PlotOrg = TRUE,
  TrajCol = FALSE, Conf = 0.95, AllBP = FALSE, TrimmingRadius = Inf,
  Partition, PrjStr, Main = "", ylab = "Feature value", alpha = 0.3,
  ScalePT = FALSE, Features = 4, facet_rows = 3, facet_cols = 3,
  Mode = "Var", ModePar = NULL, Log = FALSE, Span = 0.1, n.cores = 1,
  ClusType = "SOCK", ReturnGenes = FALSE)

`X`	the data matrix, note that features must be names, i.e. column names must be non-empty
`Paths`	a list of paths used to construct the pseudotime. Note that the beginning of the pseudotime will be placed in correspondence of the fisrst node for each path. Hence the comparison is meaningfull only if all the path begin from the same node (Although, this will not be enforced by the function)
`TargetPG`	the ElPiGraph structure to be used
`BootPG`	if not NULL, a list of resampled ElPiGraph structures that will be used to compute confidence intervals
`OnlyIsomorphicBoot`	boolean. If TRUE only reampled ElPiGraph structures with the same number of branching points of the target structure will be used to compute confidence intervals. If FALSE, all of the structures will be used.
`GroupsLab`	character of factor, category information for the cells present in the matrix.
`PlotOrg`	boolean, should the original gene expression be reported. If false oly the smooth will be plotted.
`TrajCol`	boolean, should the points be colored by trajectory? If FALSE GroupsLab will be used.
`Conf`	the confidence level.
`AllBP`	boolean. If TRUE, the confidence level be displayed for all the branching points present on the selected branches. If FALSE, the confidence level will be displayed only for the branching points
`TrimmingRadius`	numeric, the trimming radius used to project the position of the branching points of the resampled trees on the pseudotime
`Partition`	A partition vactor attributing each point to at most one node
`PrjStr`	A projecturion structure, as produced by project_point_onto_graph
`Main`	string, the main title of the plot
`ylab`	string, the label of the y axis
`alpha`	numeric between 0 and 1, the trasparency of the points
`ScalePT`	boolean, should the pseudotime be normalized across the branches?
`Features`	either a string vector or a positive integer. If a string vector, it will be interpreted as the name of the features to plot (matched to the colnames of X). If positive integer, it will be interpreted as the number of the topmost interesting features according to the metric specified by Mode
`facet_rows`	integer, the number of rows per panel
`facet_cols`	integer, the number of cols per panel
`Mode`	string, the feature seletion mode used to determine the most interesting genes. It can be 'Var' The genes with the largest variance across the points associated to the paths 'Fano' The genes with the largest Fano factor (variance over mean) across the points associated to the paths 'Mad' The genes with the largest median absolute deviation across the points associated to the paths 'Mad/Median' The genes with the largest ratio of median absolute deviation to median across the points associated to the paths 'MI' The genes with the largest mutual information (across all the paths) 'MI.DB' The genes with the largest mutual inforlation (across differential paths) 'KW' The genes with the largest difference, as computed by the Kruskal-Wallis test (across differential paths) 'Cor.DB' The genes whose product of Spearman correlation (w.r.t. the pseudotime ordering) is the largest
`ModePar`	additional parameters for the feature selection mode used
`Log`	boolean, should a log scale be used on the y axis
`Span`	the span parameter of the loess fitter
`n.cores`	integer, the number of parallel processes to use.
`ClusType`	string, the type of cluster to use if n.cores is larger than 1
`ReturnGenes`	boolean, should the list of genes be returned instead of the plots?