MOSuite-plot-pca-3D/code/main.R at 3d7d4b3d017a13e27d7045a9e732a16aa81125c1 · NIDAP-Community/MOSuite-plot-pca-3D · GitHub

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#!/usr/bin/env Rscript
rlang::global_entrace()
library(argparse)
library(glue)
library(MOSuite)
library(readr)
library(stringr)
library(dplyr)

# set up capsule environment
setup_capsule_environment()

# parse CLI arguments
parser <- ArgumentParser()

parser$add_argument("--count_type", type = "character", default = "filt")
parser$add_argument(
  "--sub_count_type",
  type = "character",
  default = NULL,
  help = "Sub count type if count_type is a list"
)
parser$add_argument(
  "--feature_id_colname",
  type = "character",
  default = NULL,
  help = "Column name for feature IDs"
)
parser$add_argument(
  "--sample_id_colname",
  type = "character",
  default = NULL,
  help = "Column name for sample IDs"
)
parser$add_argument(
  "--samples_to_rename",
  type = "character",
  default = "",
  help = "Samples to rename in format old:new,old2:new2"
)
parser$add_argument(
  "--group_colname",
  type = "character",
  default = "Group",
  help = "Column name for sample groups"
)
parser$add_argument(
  "--label_colname",
  type = "character",
  default = "Label",
  help = "Column name for sample labels"
)
parser$add_argument(
  "--principal_components",
  type = "character",
  default = "1,2,3",
  help = "Principal components to plot (comma-separated)"
)
parser$add_argument(
  "--point_size",
  type = "integer",
  default = 8,
  help = "Size of points in plot"
)
parser$add_argument(
  "--label_font_size",
  type = "integer",
  default = 24,
  help = "Font size for labels"
)
parser$add_argument(
  "--color_values",
  type = "character",
  default = "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500",
  help = "Comma-separated color values"
)
parser$add_argument(
  "--plot_title",
  type = "character",
  default = "PCA 3D",
  help = "Title for the plot"
)

args <- parser$parse_args()

# load multiOmicDataSet from data directory
moo <- load_moo_from_data_dir()

# run MOSuite
plot_pca(
  moo,
  count_type = args$count_type,
  sub_count_type = args$sub_count_type,
  principal_components = as.integer(parse_optional_vector(
    args$principal_components
  )),
  feature_id_colname = args$feature_id_colname,
  sample_id_colname = args$sample_id_colname,
  samples_to_rename = parse_samples_to_rename(args$samples_to_rename),
  group_colname = args$group_colname,
  label_colname = args$label_colname,
  point_size = args$point_size,
  label_font_size = args$label_font_size,
  color_values = parse_optional_vector(args$color_values),
  plot_title = args$plot_title
)