Plot PCA Results for Gene Expression Data — plot

This function generates a PCA plot for a `SummarizedExperiment` object using precomputed PCA results. It creates a scatter plot of the specified principal components (`pcs[1]` and `pcs[2]`). Metadata can be visualized via point color and shape.

Usage

plot_pca(
  exp_data,
  color = NA,
  shape = NA,
  fname = "results/qc/plot_PCA.pdf",
  pcs = c(1, 2),
  res_name = "pca_res",
  id_name = "sample_id",
  ellipses = FALSE,
  point_size = 2,
  out = c("plotly", "ggplot")[1]
)

Arguments

exp_data: A `SummarizedExperiment` object containing gene expression data. PCA results must be stored in `exp_data@metadata` under the name specified by `res_name`.
color: A character string specifying the column name in `colData(exp_data)` to use for coloring the points. Default is `NA`, meaning no coloring.
shape: A character string specifying the column name in `colData(exp_data)` to use for shaping the points. Default is `NA`, meaning no shaping.
fname: A character string specifying the file path to save the plot as a PDF. Default is `"results/qc/plot_PCA.pdf"`. Set to `NULL` to skip saving.
pcs: An integer vector of length 2 specifying the principal components to plot on the x and y axes. Default is `c(1, 2)`.
res_name: A character string specifying the name of the PCA results stored in `exp_data@metadata`. Default is `"pca_res"`.
id_name: A character string specifying the column name in `colData(exp_data)` containing sample identifiers. Default is `"sample_id"`.
ellipses: if TRUE, `stat_ellipse` is added to the points, representing the 0.95 confidence-interval ellipse for each group in `color`.
point_size: A numeric value specifying the size of the points in the plot. Default is `2`.
out: A character string indicating the output type: `"plotly"` (interactive Plotly plot) or `"ggplot"` (static ggplot). Default is `"plotly"`.

Value

A PCA plot, either as a `plotly` interactive object or a `ggplot` static object, depending on the `out` parameter.