Creates a boxplot to visualize pathway scores across annotations, with optional statistical comparisons and customization.
Usage
plot_path_boxplot(
exp_data,
pathway,
annotation,
color_var = NA,
pt_size = 1,
summary_type = c("choose", "line", "box")[1],
stat_comparisons = NA,
stat_format = NULL,
fname = NULL,
fwidth = 5,
fheight = 3
)Arguments
- exp_data
A `SummarizedExperiment` object containing pathway scores in the `metadata(exp_data)[["pathway_scores"]]` slot.
- pathway
A character string specifying the name of the pathway to plot.
- annotation
A character string specifying the column in `colData(exp_data)` to use for grouping samples in the plot.
- color_var
A character string specifying a column in `colData(exp_data)` to use for coloring the plot. Default is `NA` (no coloring).
- pt_size
Numeric; size of the points in the plot. Default is `1`.
- summary_type
Character; type of summary to overlay on the plot. Options are `"choose"` (default), `"line"`, or `"box"`.
- stat_comparisons
A list of character vectors specifying groups for pairwise statistical comparisons. Default is `NA` (no statistical comparisons).
- stat_format
A character string specifying the format for displaying statistical results. Default is `NULL` (no formatting).
- fname
A character string specifying the file name to save the plot. Default is `NULL` (do not save).
- fwidth
Numeric; width of the saved plot in inches. Default is `5`.
- fheight
Numeric; height of the saved plot in inches. Default is `3`.
Details
The function extracts pathway scores from the `metadata(exp_data)[["pathway_scores"]]` slot and merges them with sample annotations from `colData(exp_data)`. It generates a boxplot using a helper function `.plt_boxplot`. Statistical comparisons can be added to the plot, and the plot can be saved as an image file if `fname` is provided.
The `summary_type` argument determines the type of summary overlay:
- "choose"
No additional summary overlay.
- "line"
Adds a line connecting the median of each group.
- "box"
Adds a summary box around each group.