% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/get_QC_plots_and_stats.R
\name{get_QC_plots_parsed_merged_data}
\alias{get_QC_plots_parsed_merged_data}
\title{Plot QC plots and calculate statistics for bound data}
\usage{
get_QC_plots_parsed_merged_data(
  .data,
  list_of_columns_to_plot = NULL,
  save_plots = FALSE,
  saving_plots_folder = NULL,
  save_plots_in_patient_specific_subfolders = TRUE,
  fill_color_variable = NULL,
  PID_column_name = "PID",
  isolate_specific_drug = NULL,
  isolate_specific_patient = NULL,
  drug_column_name = "Treatment",
  save_list_of_plots = TRUE,
  p_height = 10,
  p_width = 10,
  verbose = TRUE
)
}
\arguments{
\item{.data}{The preprocessed data frame to analyze}

\item{list_of_columns_to_plot}{Columns to include in plots. If NULL, all numeric columns are used.}

\item{save_plots}{Logical, whether to save plots to files. Defaults to FALSE.}

\item{saving_plots_folder}{Directory for saving plots. If NULL and save_plots=TRUE, uses a subdirectory of tempdir().}

\item{save_plots_in_patient_specific_subfolders}{Logical, whether to create patient subdirectories. Defaults to TRUE.}

\item{fill_color_variable}{Variable name for plot color filling}

\item{PID_column_name}{Column name for patient IDs. Defaults to "PID".}

\item{isolate_specific_drug}{Drug name to subset data}

\item{isolate_specific_patient}{Patient ID to subset data}

\item{drug_column_name}{Column name for drug information. Defaults to "Treatment".}

\item{save_list_of_plots}{Logical, whether to return list of plot objects. Defaults to TRUE.}

\item{p_height}{Plot height in inches. Defaults to 10.}

\item{p_width}{Plot width in inches. Defaults to 10.}

\item{verbose}{Logical, whether to show progress messages. Defaults to TRUE.}
}
\value{
If save_list_of_plots=TRUE, returns a named list of ggplot objects. Otherwise returns invisible(NULL).
}
\description{
This function creates quality control plots and calculates basic statistics for microscopy data.
The plots provide visual insights into marker expression patterns and data quality.
}
\examples{
\donttest{
# First load and process example data
example_path <- system.file("extdata/to_merge/", package = "drugsens")
raw_data <- data_binding(path_to_the_projects_folder = example_path)
count_data <- make_count_dataframe(raw_data)
processed_data <- change_data_format_to_longer(count_data)

# Basic usage - create plots for all patients
plots <- get_QC_plots_parsed_merged_data(processed_data)

# Save plots to a temporary directory
temp_dir <- file.path(tempdir(), "qc_plots")
plots <- get_QC_plots_parsed_merged_data(
  processed_data,
  save_plots = TRUE,
  saving_plots_folder = temp_dir
)

# Focus on a specific patient
plots <- get_QC_plots_parsed_merged_data(
  processed_data,
  isolate_specific_patient = "B39"
)

# Color plots by tissue type
plots <- get_QC_plots_parsed_merged_data(
  processed_data,
  fill_color_variable = "Tissue"
)
}
}