plotTrajectory.Rd
Displays the spatial course of spatial trajectory that was
drawn with SPATA::createTrajectories()
.
plotTrajectory( object, trajectory_name, of_sample = "", color_to = NULL, method_gs = "mean", smooth = FALSE, smooth_span = 0.02, pt_size = 2.5, pt_alpha = 0.4, pt_clr = "red", pt_clrp = "milo", pt_clrsp = "inferno", sgmt_size = 1, display_image = TRUE, display_title = FALSE, uniform_genes = "discard", verbose = TRUE )
object | A valid spata-object. |
---|---|
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. |
color_to | The variable to be displayed by color:
|
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
|
smooth | Logical. If set to TRUE values will be smoothed according to the
|
smooth_span | The amount of smoothing specified as a single numeric value. |
pt_size | The size of the points specified as a single numeric value. |
pt_alpha | The transparency of the points specified as single numeric value. |
pt_clr | The base color of every point displayed in the plot. |
pt_clrp | The color panel to be used if the specified variable displayed by
color is categorical/discrete. Run |
pt_clrsp | The color spectrum to be used if the specified variable displayed by
color is continuous. Run |
sgmt_size | The size of the segment arrrow specified as a numeric value. |
display_image | Logical. If set to TRUE the histology image of the specified sample is displayed underneath the plot. |
display_title | Logical. If set to TRUE an informative title is displayed. |
uniform_genes | Character value. If set to 'discard' genes that are uniformly expressed across all barcode-spots of the specified coordinates data.frame are discarded. If set to 'keep' they are kept. |
verbose | Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
Returns a ggplot-object that can be additionally customized according to the rules of the ggplot2-framework.