% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/method.R
\name{plotFootprints}
\alias{plotFootprints}
\title{Visualize Single Molecule Footprint Patterns}
\usage{
plotFootprints(
  organism = "dmelanogaster",
  model = "S2",
  condition = "WT",
  genome_assembly = "dm6",
  type = "dSMF",
  chromosome = "chr2L",
  start = 480290,
  end = 480320,
  tr = "fp_and_mvec",
  label = "peak229",
  span_left = 150,
  span_right = 150,
  remove_dup = FALSE,
  fp_cap = 50,
  target_dir = ""
)
}
\arguments{
\item{organism}{Organism code (default: "dmelanogaster")}

\item{model}{Biological model/system (default: "S2" cells)}

\item{condition}{Experimental condition (default: "WT")}

\item{genome_assembly}{Genome version (default: "dm6")}

\item{type}{Data type ("dSMF" = dual enzyme Single Molecule Footprinting)}

\item{chromosome}{Chromosome ID (e.g., "chr2L")}

\item{start}{Genomic start position (numeric/character)}

\item{end}{Genomic end position (numeric/character)}

\item{tr}{Track name for BigBed file resource (default: "fp_and_mvec")}

\item{label}{Plot title annotation}

\item{span_left}{Upstream window size from region (default: 150)}

\item{span_right}{Downstream window size from region (default: 150)}

\item{remove_dup}{Remove duplicate reads? (default: FALSE)}

\item{fp_cap}{Maximum footprint value for y-axis scaling (default: 50)}

\item{target_dir}{destination directory where outputs will be stored}
}
\value{
Saves a heatmap in pdf, png, and eps file formats. Also, occupancies are saved in a tsv file
}
\description{
Generates footprint plots from NOME-seq data within specified genomic regions.
Designed for Drosophila melanogaster analysis with expandable parameters for other organisms.
}
\details{
This function retrieves and visualizes DNA accessibility patterns from single-molecule data:
- Integrates with UCSC-style track hubs via `tr` parameter
- Automatically handles coordinate conversion for dm6 genome
- Implements dynamic y-axis scaling using `fp_cap`
}
\examples{
# Basic usage with default parameters
plotFootprints()

# Custom genomic region analysis
plotFootprints(
  chromosome = "chr2L", start = 480290, end = 480320, label = "peak229")

}
