Compare feature values over different branches
1 2 3 4 5 6 7  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 nonempty 
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

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? 
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