pca_plot: Plots two components of a PCA

In martahidalgo/hipathia: HiPathia: High-throughput Pathway Analysis

Plots two components of a PCA

Description

Plots two components of a PCA computed with do_pca

Usage

pca_plot(
  fit,
  group = NULL,
  sample_colors = NULL,
  cp1 = 1,
  cp2 = 2,
  legend = TRUE,
  legend_xy = "bottomleft",
  cex = 2,
  pch = 20,
  mgp = c(3, 1, 0),
  main = "PCA plot",
  save_png = NULL
)

Arguments

fit	princomp object as returned by do_pca
group	Vector with the group to which each sample belongs. The samples must be ordered as in rownames(fit$scores). By default, all samples will be assigned to the same class.
sample_colors	Named character vector of colors. The names of the colors must be the classes in group. Each sample will be assigned the color corresponding to its class, taken from the group vector. By default a color will be assigned automatically to each class.
cp1	Integer, number of the component in the X-axis. Default is 1, the first component.
cp2	Integer, number of the component in the Y-axis. Default is 2, the second component.
legend	Boolean, whether to plot a legend in the plot. Default is TRUE.
legend_xy	Situation of the legend in the plot. Available options are: "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center".
cex	Graphical parameter from par() function.
pch	Graphical parameter from par() function.
mgp	Graphical parameter from par() function.
main	Title of the graphics
save_png	Path to the file where the image as PNG will be saved. By default, the image is not saved.

Value

Plots two components of a PCA

Examples

data(path_vals)
sample_group <- brca_design[colnames(path_vals),"group"]
pca_model <- do_pca(path_vals[seq_len(ncol(path_vals)),])
pca_plot(pca_model, sample_group)

martahidalgo/hipathia documentation built on Jan. 12, 2023, 1:44 p.m.