plotTrajectoryHeatmap.Rd
Displays variable-expression values along a trajectory direction with a smoothed heatmap (from left to right).
plotTrajectoryHeatmap( object, trajectory_name, of_sample = "", variables, method_gs = "mean", arrange_rows = "none", show_rownames = FALSE, show_colnames = FALSE, split_columns = TRUE, smooth_span = 0.5, verbose = TRUE, hm_colors = viridis::inferno(150), ... )
object | A valid spata-object. |
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trajectory_name | The trajectory of interest specified as a single character value. |
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. |
variables | The variables of interest specified as a character vector:
All elements of the specified character vector must either belong to gene sets or to genes. |
arrange_rows | Alter the way the rows of the heatmap are displayed in order to highlight patterns. Currently either 'maxima' or 'minima'. |
show_rownames | Logical. If set to TRUE the variable elements will be displayed at the rownames of the heatmap. |
split_columns | Logial. If set to TRUE the heatmap is vertically splitted according to the trajectory parts. |
smooth_span | The amount of smoothing specified as a single numeric value. |
verbose | Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
hm_colors | A vector of colors to be used. |
... | Additional parameters given to |
A heatmap of class 'pheatmap'.