plotTrajectoryFeatures.Rd
Displays values along a trajectory direction with a smoothed lineplot.
plotTrajectoryFeatures( object, trajectory_name, of_sample = "", features = "percent.mt", smooth_method = "loess", smooth_span = 0.2, smooth_se = TRUE, clrp = "milo", verbose = TRUE ) plotTrajectoryFeaturesDiscrete( object, trajectory_name, of_sample = "", discrete_feature, clrp = "milo", display_trajectory_parts = FALSE, verbose = TRUE, ... ) plotTrajectoryGenes( object, trajectory_name, of_sample = "", genes, clrp = "milo", average_genes = FALSE, smooth_method = "loess", smooth_span = 0.2, smooth_se = TRUE, display_trajectory_parts = TRUE, verbose = TRUE ) plotTrajectoryGeneSets( object, trajectory_name, of_sample = "", gene_sets = "Neftel_NPC_Comb", method_gs = "mean", smooth_method = "loess", smooth_span = 0.2, smooth_se = TRUE, clrp = "milo", display_trajectory_parts = TRUE, verbose = TRUE )
object | A valid spata-object. |
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of_sample | The sample(s) of interest specified as a single character value or vector. If set to "" (the default) the first sample is chosen. |
features | The features of interest specified as a character vector. |
smooth_method | The smoothing method that will be used specified as a single character value (e.g. "lm", "glm", "gam", "loess"). |
smooth_span | The amount of smoothing specified as a single numeric value. |
smooth_se | Logical. If set to TRUE the confidence interval will be displayed. |
clrp | Character value. The color panel to be used.
Run |
verbose | Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
discrete_feature | Character value. The discrete feature of interest. |
display_trajectory_parts | Logical. If set to TRUE the returned plot visualizes the parts in which the trajectory has been partitioned while beeing drawn. |
genes | The genes of interest specified as a character vector. |
average_genes | Logical value. If set to TRUE the mean expression of all specified genes will be calculated. |
gene_sets | The gene sets of interest specified as a character vector. |
method_gs | Character value. The method according to which gene sets will be handled
specified as a character of length one. This can be either 'mean' or one
of 'gsva', 'ssgsea', 'zscore', or 'plage'. The latter four will be given to
|
Returns a ggplot-object that can be additionally customized according to the rules of the ggplot2-framework.