Creates a scatter plot comparing scores for two pathways from the pathway scores stored in the metadata of a given dataset. Optionally saves the plot to a file.
Usage
plot_path_scatter(
exp_data,
pathway1,
pathway2,
color_var = NA,
pt_size = 2,
fname = NULL,
fwidth = 5,
fheight = 3
)Arguments
- exp_data
An object containing experimental data. Must include pathway scores in `metadata(exp_data)[["pathway_scores"]]`.
- pathway1
A string specifying the name of the first pathway for comparison.
- pathway2
A string specifying the name of the second pathway for comparison.
- color_var
(Optional) A variable used to color points in the scatter plot. Default is `NA`.
- pt_size
A numeric value specifying the size of points in the scatter plot. Default is `2`.
- fname
(Optional) A string specifying the file name to save the plot. If `NULL`, the plot is not saved. Default is `NULL`.
- fwidth
A numeric value specifying the width of the saved plot in inches. Default is `5`.
- fheight
A numeric value specifying the height of the saved plot in inches. Default is `3`.
Details
This function extracts pathway scores from the metadata of the provided experimental data object, then creates a scatter plot comparing the scores of the specified pathways. An optional variable can be used to color the points. If a file name is provided, the plot is saved to the specified location.