## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(lisat)

## ----generate_data------------------------------------------------------------
set.seed(12345)

n_rows <- 10000
sample_names <- c("Sample_A", "Sample_B", "Sample_C")
chr_list <- paste0(1:23)

# Generate random data
Sample <- sample(sample_names, size = n_rows, replace = TRUE)
SCount <- sample(1:1000, size = n_rows, replace = TRUE)
Chr <- sample(chr_list, size = n_rows, replace = TRUE)
Locus <- sample(1:150000000, size = n_rows, replace = TRUE)

IS_raw <- data.frame(
  Sample = Sample,
  SCount = SCount,
  Chr = Chr,
  Locus = Locus,
  stringsAsFactors = FALSE
)

# Simulate some high-frequency clones (updated)
IS_raw$SCount[1:100] <- sample(500000:800000, 100, replace = TRUE)

head(IS_raw)

## ----validate_data------------------------------------------------------------
check_validity <- validate_IS_raw(IS_raw)

## ----patient_meta-------------------------------------------------------------
Patient_timepoint <- data.frame(
  Sample_ID = c("Sample_A", "Sample_B", "Sample_C"),
  Time_Point = c("3m", "12m", "24m"),
  Patient_ID = rep("Pt1", 3),
  stringsAsFactors = FALSE
)

head(Patient_timepoint)

## ----get_features, message=FALSE, warning=FALSE-------------------------------
if (requireNamespace("TxDb.Hsapiens.UCSC.hg38.knownGene", quietly = TRUE) &&
    requireNamespace("org.Hs.eg.db", quietly = TRUE)) {
    
  IS_raw <- get_feature(IS_raw)
  
  # Check for overlap with specific genomic elements
  IS_raw <- Enhancer_check(IS_raw)
  IS_raw <- Promotor_check(IS_raw)
  IS_raw <- Safeharbor_check(IS_raw)
  
  names(IS_raw)
} else {
  message("Skipping annotation: Required annotation packages not installed.")
}

## ----cis_analysis-------------------------------------------------------------
CIS_top <- CIS(IS_raw = IS_raw, connect_distance = 50000)
CIS_by_sample <- CIS_overlap(CIS_data = CIS_top, IS_raw = IS_raw)
CIS_by_sample

## ----chr_dist, fig.width=10, fig.height=7, out.width="100%"-------------------
chr_stats <- chr_distribution(IS_raw)
print(chr_stats)

## ----gene_sets, fig.width=10, fig.height=8, out.width="100%"------------------
if (requireNamespace("TxDb.Hsapiens.UCSC.hg38.knownGene", quietly = TRUE) &&
    requireNamespace("org.Hs.eg.db", quietly = TRUE)) {
  # Adverse Event genes
  ae_overlap <- is_in_AE_gene(IS_raw = IS_raw, Distance = 100000)
  
  # Cancer Genes
  cg_overlap <- is_in_CG_gene(IS_raw = IS_raw, threashold = 0.001)
  print(cg_overlap)
  
  # Immune Genes
  immune_overlap <- is_in_immune_gene(IS_raw = IS_raw, threashold = 0.001)
}

## ----pmd_analysis, fig.width=10, fig.height=7, out.width="100%"---------------
PMD_data <- pmd_analysis(IS_raw = IS_raw, Patient_timepoint = Patient_timepoint)
head(PMD_data)
# Plot Richness and Evenness
plot_richness_evenness(PMD_data = PMD_data)

# Analyze linked timepoints
linked_data <- Linked_timepoints(IS_raw = IS_raw, Patient_timepoint = Patient_timepoint)
print(linked_data)

## ----clonal_dominance, fig.width=10, fig.height=6, out.width="100%"-----------
IS_ratio <- fit_cum_simple(IS_raw$SCount)
print(Cumulative_curve(IS_ratio)) # Function for plotting

## ----treemap, fig.width=10, fig.height=8, out.width="100%"--------------------
if (requireNamespace("treemapify", quietly = TRUE)) {
    IS_treemap(IS_raw = IS_raw, Patient_timepoint = Patient_timepoint)
}

## ----region_counts, fig.width=10, fig.height=7, out.width="100%"--------------
Region_data <- Count_regions(IS_raw = IS_raw, Patient_timepoint = Patient_timepoint)
head(Region_data)
plot_regions(Region_data = Region_data)

## ----ideogram, eval=FALSE-----------------------------------------------------
#  # Example usage:
#  # ideogram_plot(IS_raw, output_dir = tempdir())