diff --git a/codecov.yml b/.github/codecov.yml
similarity index 100%
rename from codecov.yml
rename to .github/codecov.yml
diff --git a/DESCRIPTION b/DESCRIPTION
index 89d243a..f15d3dc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -39,15 +39,17 @@ Imports:
     tidyselect,
     plotly,
     scico,
-    magick (>= 2.9.0),
-    tinytex (>= 0.58)
+    rmarkdown
 Suggests:
     covr,
     testthat (>= 3.0.0),
     withr,
+    spelling,
     knitr,
-    rmarkdown,
-    spelling
+    magick (>= 2.9.0),
+    tinytex (>= 0.58),
+    gridExtra,
+    grid
 Config/testthat/edition: 3
 URL: https://cabajr.github.io/ClockCyteR.spatial/
 Language: en-US
diff --git a/R/modules_foo.R b/R/modules_foo.R
index 4fe86ec..1b480b0 100644
--- a/R/modules_foo.R
+++ b/R/modules_foo.R
@@ -1121,11 +1121,16 @@ validate_params <- function(p) {
 
 #' generate_reports
 #'
-#' Renders a per-file HTML or PDF report for each file in the project,
-#' collecting all plot types across intervals and channels.
+#' Renders a per-file report for each file in the project, collecting all plot
+#' types across intervals and channels. Output is HTML by default (no system
+#' dependencies); set \code{pdf = TRUE} for PDF output (requires additional
+#' system dependencies — see Details).
 #'
 #' @param params A named list of analysis parameters as produced by \code{make_params()}.
 #' @param file_rows A tibble of file metadata as produced by \code{index_files()}.
+#' @param pdf Logical; if \code{TRUE} render PDF reports instead of HTML.
+#'   Requires \pkg{magick}, \pkg{tinytex}, and a TinyTeX installation
+#'   (\code{tinytex::install_tinytex()}). Defaults to \code{FALSE}.
 #'
 #' @return Called for its side effects (report files written to disk). Returns
 #'   \code{NULL} invisibly.
@@ -1134,80 +1139,96 @@ validate_params <- function(p) {
 #' @examples
 #' \dontrun{
 #' generate_reports(params, file_rows)
+#' generate_reports(params, file_rows, pdf = TRUE)
 #' }
-generate_reports <- function(params, file_rows) {
-  intervals <- names(params$time$intervals)
-  channels <- names(params$channels)
-  plot_types <- c(params$plotting$plot_types, params$plotting$network_plot_types)
-  base_dir <- params$paths$base_dir
+generate_reports <- function(params, file_rows, pdf = FALSE) {
+  intervals   <- names(params$time$intervals)
+  channels    <- names(params$channels)
+  plot_types  <- c(params$plotting$plot_types, params$plotting$network_plot_types)
+  base_dir    <- params$paths$base_dir
   reports_dir <- file.path(base_dir, "reports")
 
   if (!dir.exists(reports_dir)) dir.create(reports_dir)
 
   n_files <- length(file_rows$file_id)
-  pb_id <- cli::cli_progress_bar("Generating reports", total = n_files)
+  pb_id   <- cli::cli_progress_bar("Generating reports", total = n_files)
 
-  purrr::walk(file_rows$file_id, function(fid){
+  purrr::walk(file_rows$file_id, function(fid) {
     generate_file_report(
-    file_id =fid,
-    params = params,
-    base_dir = base_dir,
-    intervals = intervals,
-    channels = channels,
-    plot_types = plot_types
-  )
+      file_id    = fid,
+      params     = params,
+      base_dir   = base_dir,
+      intervals  = intervals,
+      channels   = channels,
+      plot_types = plot_types,
+      pdf        = pdf
+    )
     cli::cli_progress_update(id = pb_id)
-    })
+  })
+
   cli::cli_progress_done(id = pb_id)
   message("Reports generated.")
 }
 
 #' generate_plot_type_reports
 #'
-#' Renders one PDF report per plot type, collating the corresponding plot
-#' across all files, intervals, and channels using an Rmd template.
+#' Renders one report per plot type, collating the corresponding plot across
+#' all files, intervals, and channels using an Rmd template. Output is HTML
+#' by default; set \code{pdf = TRUE} for PDF output (requires additional
+#' system dependencies — see Details).
 #'
 #' @param params A named list of analysis parameters as produced by \code{make_params()}.
 #' @param file_rows A tibble of file metadata as produced by \code{index_files()}.
 #' @param storage_fold Character string naming the subfolder within each
 #'   file's results directory where plots are stored. Defaults to
 #'   \code{"plots"}.
-#' @param plot_report_template Character string giving the filename of the Rmd
-#'   template to use. Defaults to \code{"plot_type_report_template.Rmd"}.
 #' @param plot_report_dir Character string giving the output directory for
 #'   rendered reports. Defaults to \code{file.path(params$paths$base_dir,
 #'   "reports", "plot_reports")}.
+#' @param pdf Logical; if \code{TRUE} render PDF reports instead of HTML.
+#'   Requires \pkg{magick}, \pkg{tinytex}, and a TinyTeX installation
+#'   (\code{tinytex::install_tinytex()}). Defaults to \code{FALSE}.
 #'
-#' @return Called for its side effects (PDF reports written to
+#' @return Called for its side effects (reports written to
 #'   \code{plot_report_dir}). Returns \code{NULL} invisibly.
 #' @export
 #'
 #' @examples
 #' \dontrun{
 #' generate_plot_type_reports(params, file_rows)
+#' generate_plot_type_reports(params, file_rows, pdf = TRUE)
 #' }
 generate_plot_type_reports <- function(
     params,
     file_rows,
-    storage_fold = "plots",
-    plot_report_template = "plot_type_report_template.Rmd",
-    plot_report_dir = file.path(params$paths$base_dir, "reports", "plot_reports")
+    storage_fold    = "plots",
+    plot_report_dir = file.path(params$paths$base_dir, "reports", "plot_reports"),
+    pdf             = FALSE
 ) {
-  intervals   <- names(params$time$intervals)
-  channels    <- names(params$channels)
-  plot_types  <- c(params$plotting$plot_types, params$plotting$network_plot_types)
-  base_dir    <- params$paths$base_dir
+  if (pdf) {
+    check_pdf_deps()
+    plot_report_template <- "plot_type_report_template_pdf.Rmd"
+    output_ext           <- ".pdf"
+  } else {
+    plot_report_template <- "plot_type_report_template.Rmd"
+    output_ext           <- ".html"
+  }
+
+  intervals  <- names(params$time$intervals)
+  channels   <- names(params$channels)
+  plot_types <- c(params$plotting$plot_types, params$plotting$network_plot_types)
+  base_dir   <- params$paths$base_dir
 
   if (!dir.exists(plot_report_dir)) dir.create(plot_report_dir, recursive = TRUE)
 
   n_plot_types <- length(plot_types)
-  pb_id <- cli::cli_progress_bar("Generating plot-type reports", total = n_plot_types)
+  pb_id        <- cli::cli_progress_bar("Generating plot-type reports", total = n_plot_types)
 
   purrr::walk(plot_types, function(pt) {
     rmarkdown::render(
-      input = system.file("rmd", plot_report_template, package = "ClockCyteR.spatial"),
-      output_file = file.path(plot_report_dir, paste0("plot_report_", pt, ".pdf")),
-      params = list(
+      input       = system.file("rmd", plot_report_template, package = "ClockCyteR.spatial"),
+      output_file = file.path(plot_report_dir, paste0("plot_report_", pt, output_ext)),
+      params      = list(
         channel_params = params$channels,
         file_rows      = file_rows,
         base_dir       = base_dir,
diff --git a/R/utils_foo.R b/R/utils_foo.R
index 66df908..cf31f16 100644
--- a/R/utils_foo.R
+++ b/R/utils_foo.R
@@ -248,6 +248,34 @@ extract_vars <- function(params, file_rows, vars, network = FALSE, individual =
 
 }
 
+check_pdf_deps <- function() {
+  missing_pkgs <- character(0)
+  if (!requireNamespace("magick",    quietly = TRUE)) missing_pkgs <- c(missing_pkgs, "magick")
+  if (!requireNamespace("tinytex",   quietly = TRUE)) missing_pkgs <- c(missing_pkgs, "tinytex")
+  if (!requireNamespace("gridExtra", quietly = TRUE)) missing_pkgs <- c(missing_pkgs, "gridExtra")
+
+  if (length(missing_pkgs) > 0) {
+    stop(
+      "PDF report generation requires additional packages: ",
+      paste(missing_pkgs, collapse = ", "), ".\n",
+      "Install them with: install.packages(c(",
+      paste0('"', missing_pkgs, '"', collapse = ", "), "))",
+      call. = FALSE
+    )
+  }
+
+  if (!tinytex::is_tinytex()) {
+    stop(
+      "TinyTeX (LaTeX) is not installed. PDF generation requires it.\n",
+      "Install it with: tinytex::install_tinytex()\n",
+      "Or use the default HTML output by leaving pdf = FALSE.",
+      call. = FALSE
+    )
+  }
+
+  invisible(TRUE)
+}
+
 #' Render an Rmd report for a single file
 #'
 #' @param file_id Character; file identifier.
@@ -259,12 +287,13 @@ extract_vars <- function(params, file_rows, vars, network = FALSE, individual =
 #'   report.
 #' @param storage_fold Character; subdirectory containing the plots. Defaults
 #'   to \code{"plots"}.
-#' @param report_template Character; filename of the Rmd template. Defaults
-#'   to \code{"report_template.Rmd"}.
 #' @param output_dir Character; directory where the rendered report is saved.
 #'   Defaults to a \code{reports} subdirectory inside \code{base_dir}.
+#' @param pdf Logical; if \code{TRUE} render a PDF instead of HTML. Requires
+#'   \pkg{magick}, \pkg{tinytex}, and a TinyTeX installation. Defaults to
+#'   \code{FALSE}.
 #'
-#' @return Called for its side effect of rendering an HTML report; returns
+#' @return Called for its side effect of rendering a report; returns
 #'   the output file path invisibly.
 #' @keywords internal
 generate_file_report <- function(
@@ -275,9 +304,17 @@ generate_file_report <- function(
     channels,
     plot_types,
     storage_fold = "plots",
-    report_template = "report_template.Rmd",
-    output_dir = file.path(base_dir, "reports")
+    output_dir   = file.path(base_dir, "reports"),
+    pdf          = FALSE
 ) {
+  if (pdf) {
+    check_pdf_deps()
+    report_template <- "report_template_pdf.Rmd"
+    output_ext      <- ".pdf"
+  } else {
+    report_template <- "report_template.Rmd"
+    output_ext      <- ".html"
+  }
   # Build period summary path
   period_summary_path <- file.path(base_dir, paste0(file_id, "_results"),
                                    "rds",
@@ -307,7 +344,7 @@ generate_file_report <- function(
   # Render the report
   rmarkdown::render(
     input = system.file("rmd", report_template, package = "ClockCyteR.spatial"),
-    output_file = file.path(output_dir, paste0("report_", file_id, ".pdf")),
+    output_file = file.path(output_dir, paste0("report_", file_id, output_ext)),
     params = list(
       channel_params = params$channels,
       file_id = file_id,
diff --git a/inst/rmd/plot_type_report_template.Rmd b/inst/rmd/plot_type_report_template.Rmd
index cd44f46..f375615 100644
--- a/inst/rmd/plot_type_report_template.Rmd
+++ b/inst/rmd/plot_type_report_template.Rmd
@@ -1,6 +1,10 @@
 ---
 title: "Plot Type Report: `r params$plot_type`"
-output: pdf_document
+output:
+  html_document:
+    self_contained: true
+    toc: true
+    toc_float: true
 params:
   channel_params: NULL
   file_rows: NULL
@@ -11,33 +15,16 @@ params:
   save_format: NULL
 ---
 
-
 ```{r setup, include=FALSE}
 library(knitr)
-library(magick)
-library(dplyr)
-library(gridExtra)
-library(grid)
-
-knitr::opts_chunk$set(
-  echo = FALSE,
-  warning = FALSE,
-  message = FALSE
-)
-
+knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE)
 ```
 
----
-
-
-##
-## Plots by Type, Interval and Channel
-
-```{r params$plot_type, results='asis', fig.width=8, fig.height=8}
-
-plot_type <- params$plot_type
-plot_name <- plot_type_to_name(plot_type)
+## Plots by Channel and Interval
 
+```{r plots, results='asis'}
+plot_type      <- params$plot_type
+plot_name      <- plot_type_to_name(plot_type)
 base_dir       <- params$base_dir
 intervals      <- params$intervals
 channels       <- params$channels
@@ -45,107 +32,45 @@ file_rows      <- params$file_rows
 channel_params <- params$channel_params
 save_format    <- params$save_format
 
-# Enabled channels only
-enabled_channels <- names(Filter(function(ch) ch$enabled, channel_params))
-channels <- intersect(channels, enabled_channels)
-
-# Check if multiple intervals
+enabled_channels   <- names(Filter(function(ch) ch$enabled, channel_params))
+channels           <- intersect(channels, enabled_channels)
 multiple_intervals <- length(intervals) > 1
 
-# Loop: channel -> interval -> files
 for (channel in channels) {
-  cat("\n\n# Channel: ", channel, ": ", params$channel_params[[channel]]$label, "\n\n", sep = "")
-  
+  cat("\n\n# Channel:", channel, "—", channel_params[[channel]]$label, "\n\n")
+
   for (interval in intervals) {
-    # Only show interval header if multiple intervals
     if (multiple_intervals) {
-      cat("\n\n## Interval: ", interval, "\n\n", sep = "")
+      cat("\n\n## Interval:", interval, "\n\n")
     }
-    
-    # Collect all grobs for this channel and interval across all files
-    grobs <- list()
-    grob_labels <- character(0)
-    
+
+    found_any <- FALSE
+
     for (fid in file_rows$file_id) {
-      # Conditional path construction based on number of intervals
       if (multiple_intervals) {
-        ch_id_folder <- file.path(
-          base_dir,
-          paste0(fid, "_results"),
-          "plots",
-          interval,
-          channel
-        )
+        ch_id_folder <- file.path(base_dir, paste0(fid, "_results"),
+                                  "plots", interval, channel)
       } else {
-        ch_id_folder <- file.path(
-          base_dir,
-          paste0(fid, "_results"),
-          "plots",
-          channel
-        )
+        ch_id_folder <- file.path(base_dir, paste0(fid, "_results"),
+                                  "plots", channel)
       }
-      
-      plot_path <- build_plot_path(
-        file_id      = fid,
-        ch_id        = channel,
-        ch_id_folder = ch_id_folder,
-        plot_name    = plot_name,
-        save_format  = save_format
-      )
-      
+
+      plot_path <- build_plot_path(file_id      = fid,
+                                   ch_id        = channel,
+                                   ch_id_folder = ch_id_folder,
+                                   plot_name    = plot_name,
+                                   save_format  = save_format)
+
       if (file.exists(plot_path)) {
-        img <- magick::image_read_svg(plot_path)
-        png_path <- tempfile(fileext = ".png")
-        magick::image_write(img, path = png_path, format = "png", density = 300)
-        
-        grobs[[length(grobs) + 1]] <- grid::rasterGrob(magick::image_read(png_path))
-        grob_labels <- c(grob_labels, paste0("File: ", fid))
-      }
-    } # file
-    
-    # Arrange plots for this interval in 3x4 grids (12 per page)
-    n_plots <- length(grobs)
-    if (n_plots > 0) {
-      for (i in seq(1, n_plots, by = 12)) {
-        grid_grobs  <- grobs[i:min(i + 11, n_plots)]
-        grid_labels <- grob_labels[i:min(i + 11, n_plots)]
-        
-        # Conditional title based on number of intervals
-        if (multiple_intervals) {
-          grid_title <- paste0(
-            "Plot type: ", plot_type,
-            "   |   Channel: ", channel,
-            "   |   Interval: ", interval,
-            "\n\nShowing plots ", i, "-", min(i + 11, n_plots),
-            " of ", n_plots
-          )
-        } else {
-          grid_title <- paste0(
-            "Plot type: ", plot_type,
-            "   |   Channel: ", channel,
-            "\n\nShowing plots ", i, "-", min(i + 11, n_plots),
-            " of ", n_plots
-          )
-        }
-        
-        gridExtra::grid.arrange(
-          grobs = grid_grobs,
-          ncol  = 3,
-          nrow  = 4,
-          top   = grid_title
-        )
-        cat("\\newpage\n")
-      }
-    } else {
-      if (multiple_intervals) {
-        cat("*No plots found for this interval.*\n\n")
-      } else {
-        cat("*No plots found.*\n\n")
+        found_any <- TRUE
+        cat(paste0("\n\n### File: ", fid, "\n\n"))
+        svg_content <- paste(readLines(plot_path, warn = FALSE), collapse = "\n")
+        cat(svg_content, "\n\n")
       }
     }
-  } # interval
-} # channel
 
+    if (!found_any) cat("*No plots found.*\n\n")
+    cat("<hr>\n")
+  }
+}
 ```
-
-
diff --git a/inst/rmd/plot_type_report_template_pdf.Rmd b/inst/rmd/plot_type_report_template_pdf.Rmd
new file mode 100644
index 0000000..4cbbd9f
--- /dev/null
+++ b/inst/rmd/plot_type_report_template_pdf.Rmd
@@ -0,0 +1,101 @@
+---
+title: "Plot Type Report: `r params$plot_type`"
+output: pdf_document
+params:
+  channel_params: NULL
+  file_rows: NULL
+  base_dir: NULL
+  intervals: NULL
+  channels: NULL
+  plot_type: NULL
+  save_format: NULL
+---
+
+```{r setup, include=FALSE}
+library(knitr)
+library(magick)
+library(dplyr)
+library(gridExtra)
+library(grid)
+knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE)
+```
+
+## Plots by Channel and Interval
+
+```{r plots, results='asis', fig.width=8, fig.height=8}
+plot_type      <- params$plot_type
+plot_name      <- plot_type_to_name(plot_type)
+base_dir       <- params$base_dir
+intervals      <- params$intervals
+channels       <- params$channels
+file_rows      <- params$file_rows
+channel_params <- params$channel_params
+save_format    <- params$save_format
+
+enabled_channels   <- names(Filter(function(ch) ch$enabled, channel_params))
+channels           <- intersect(channels, enabled_channels)
+multiple_intervals <- length(intervals) > 1
+
+for (channel in channels) {
+  cat("\n\n# Channel:", channel, ":", channel_params[[channel]]$label, "\n\n")
+
+  for (interval in intervals) {
+    if (multiple_intervals) {
+      cat("\n\n## Interval:", interval, "\n\n")
+    }
+
+    grobs       <- list()
+    grob_labels <- character(0)
+
+    for (fid in file_rows$file_id) {
+      if (multiple_intervals) {
+        ch_id_folder <- file.path(base_dir, paste0(fid, "_results"),
+                                  "plots", interval, channel)
+      } else {
+        ch_id_folder <- file.path(base_dir, paste0(fid, "_results"),
+                                  "plots", channel)
+      }
+
+      plot_path <- build_plot_path(file_id      = fid,
+                                   ch_id        = channel,
+                                   ch_id_folder = ch_id_folder,
+                                   plot_name    = plot_name,
+                                   save_format  = save_format)
+
+      if (file.exists(plot_path)) {
+        img      <- magick::image_read_svg(plot_path)
+        png_path <- tempfile(fileext = ".png")
+        magick::image_write(img, path = png_path, format = "png", density = 300)
+        grobs[[length(grobs) + 1]] <- grid::rasterGrob(magick::image_read(png_path))
+        grob_labels <- c(grob_labels, paste0("File: ", fid))
+      }
+    }
+
+    n_plots <- length(grobs)
+    if (n_plots > 0) {
+      for (i in seq(1, n_plots, by = 12)) {
+        grid_grobs  <- grobs[i:min(i + 11, n_plots)]
+        grid_labels <- grob_labels[i:min(i + 11, n_plots)]
+
+        if (multiple_intervals) {
+          grid_title <- paste0("Plot type: ", plot_type,
+                               "   |   Channel: ", channel,
+                               "   |   Interval: ", interval,
+                               "\n\nShowing plots ", i, "-", min(i + 11, n_plots),
+                               " of ", n_plots)
+        } else {
+          grid_title <- paste0("Plot type: ", plot_type,
+                               "   |   Channel: ", channel,
+                               "\n\nShowing plots ", i, "-", min(i + 11, n_plots),
+                               " of ", n_plots)
+        }
+
+        gridExtra::grid.arrange(grobs = grid_grobs, ncol = 3, nrow = 4, top = grid_title)
+        cat("\\newpage\n")
+      }
+    } else {
+      cat("*No plots found.*\n\n")
+    }
+  }
+}
+```
diff --git a/inst/rmd/report_template.Rmd b/inst/rmd/report_template.Rmd
index eaa630d..b7dd664 100644
--- a/inst/rmd/report_template.Rmd
+++ b/inst/rmd/report_template.Rmd
@@ -1,6 +1,10 @@
 ---
 title: "Analysis Report for `r params$file_id`"
-output: pdf_document
+output:
+  html_document:
+    self_contained: true
+    toc: true
+    toc_float: true
 params:
   channel_params: NULL
   file_id: NULL
@@ -14,118 +18,67 @@ params:
   save_format: NULL
 ---
 
-
 ```{r setup, include=FALSE}
 library(knitr)
-library(magick)
 library(dplyr)
-library(gridExtra)
-library(grid)
 knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE)
-
 ```
 
----
-
-### **B. Period Summary Table (visible output):**
-
-
-## Period Table Summary
+## Period Summary
 
 ```{r period-summary}
 period_summary <- read.csv(params$period_summary_path)
-knitr::kable(t(period_summary)[-1,], caption = "Period Table Summary")
-
+knitr::kable(t(period_summary)[-1, ], caption = "Period Table Summary")
 ```
----
 
-### **C. Plots by Interval and Channel (visible output):**
+---
 
 ## Plots by Interval and Channel
 
-```{r plots-by-interval, results='asis', fig.width=8, fig.height=8}
-# Check if multiple intervals
+```{r plots-by-interval, results='asis'}
 multiple_intervals <- length(params$intervals) > 1
 
 for (interval in params$intervals) {
-  # Only show interval header if multiple intervals
   if (multiple_intervals) {
-    cat("\n\n## Interval: ", interval, "\n\n")
+    cat("\n\n## Interval:", interval, "\n\n")
   }
-  
+
   for (channel in params$channels) {
-    if(!params$channel_params[[channel]]$enabled) next
-    cat("### Channel: ", channel,": ", params$channel_params[[channel]]$label, "\n\n")
-    
+    if (!params$channel_params[[channel]]$enabled) next
+    cat("### Channel:", channel, "—", params$channel_params[[channel]]$label, "\n\n")
+
     plot_types <- names(params$plot_paths[[interval]][[channel]])
-    grobs <- list()
-    grob_labels <- c()
-    
+    found_any  <- FALSE
+
     for (plot_type in plot_types) {
       plot_name <- plot_type_to_name(plot_type)
-      
-      # Conditional path construction based on number of intervals
+
       if (multiple_intervals) {
-        ch_id_folder <- file.path(params$base_dir, 
-                                  paste0(params$file_id, "_results"), 
-                                  "plots",
-                                  interval,
-                                  channel)
+        ch_id_folder <- file.path(params$base_dir,
+                                  paste0(params$file_id, "_results"),
+                                  "plots", interval, channel)
       } else {
-        ch_id_folder <- file.path(params$base_dir, 
-                                  paste0(params$file_id, "_results"), 
-                                  "plots",
-                                  channel)
+        ch_id_folder <- file.path(params$base_dir,
+                                  paste0(params$file_id, "_results"),
+                                  "plots", channel)
       }
-      
-      plot_path <- build_plot_path(file_id = params$file_id,
-                                   ch_id = channel,
+
+      plot_path <- build_plot_path(file_id      = params$file_id,
+                                   ch_id        = channel,
                                    ch_id_folder = ch_id_folder,
-                                   plot_name = plot_name,
-                                   save_format = params$save_format)
-      
+                                   plot_name    = plot_name,
+                                   save_format  = params$save_format)
+
       if (file.exists(plot_path)) {
-        img <- magick::image_read_svg(plot_path)
-        png_path <- tempfile(fileext = ".png")
-        magick::image_write(img, path = png_path, format = "png", density = 300)
-        grobs[[length(grobs) + 1]] <- grid::rasterGrob(magick::image_read(png_path))
-        grob_labels <- c(grob_labels, plot_type)
-      } 
-    }
-    
-    # Arrange in grids of 4
-    n_plots <- length(grobs)
-    if (n_plots > 0) {
-      for (i in seq(1, n_plots, by = 4)) {
-        grid_grobs <- grobs[i:min(i+3, n_plots)]
-        grid_labels <- grob_labels[i:min(i+3, n_plots)]
-        
-        # Conditional title
-        if (multiple_intervals) {
-          grid_title <- paste0("Interval: ", interval, " | Plots: ", 
-                              paste(grid_labels, collapse = ", "), "\n")
-        } else {
-          grid_title <- paste0("Plots: ", paste(grid_labels, collapse = ", "), "\n")
-        }
-        
-        gridExtra::grid.arrange(grobs = grid_grobs,
-                                ncol = 2, nrow = 2,
-                                top = grid_title)
-        cat("\\newpage\n")
+        found_any <- TRUE
+        cat(paste0("\n\n#### ", plot_type, "\n\n"))
+        svg_content <- paste(readLines(plot_path, warn = FALSE), collapse = "\n")
+        cat(svg_content, "\n\n")
       }
-    } else {
-      cat("*No plots found for this channel.*\n\n")
     }
-  }
-  
-  # Add page break between intervals if multiple
-  if (multiple_intervals) {
-    cat("\\newpage\n")
+
+    if (!found_any) cat("*No plots found for this channel.*\n\n")
+    cat("<hr>\n")
   }
 }
-
 ```
-
-
----
-
diff --git a/inst/rmd/report_template_pdf.Rmd b/inst/rmd/report_template_pdf.Rmd
new file mode 100644
index 0000000..787d124
--- /dev/null
+++ b/inst/rmd/report_template_pdf.Rmd
@@ -0,0 +1,104 @@
+---
+title: "Analysis Report for `r params$file_id`"
+output: pdf_document
+params:
+  channel_params: NULL
+  file_id: NULL
+  period_summary_path: NULL
+  plot_paths: NULL
+  intervals: NULL
+  channels: NULL
+  file_rows: NULL
+  base_dir: NULL
+  plot_types: NULL
+  save_format: NULL
+---
+
+```{r setup, include=FALSE}
+library(knitr)
+library(magick)
+library(dplyr)
+library(gridExtra)
+library(grid)
+knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE)
+```
+
+## Period Summary
+
+```{r period-summary}
+period_summary <- read.csv(params$period_summary_path)
+knitr::kable(t(period_summary)[-1, ], caption = "Period Table Summary")
+```
+
+---
+
+## Plots by Interval and Channel
+
+```{r plots-by-interval, results='asis', fig.width=8, fig.height=8}
+multiple_intervals <- length(params$intervals) > 1
+
+for (interval in params$intervals) {
+  if (multiple_intervals) {
+    cat("\n\n## Interval:", interval, "\n\n")
+  }
+
+  for (channel in params$channels) {
+    if (!params$channel_params[[channel]]$enabled) next
+    cat("### Channel:", channel, ":", params$channel_params[[channel]]$label, "\n\n")
+
+    plot_types  <- names(params$plot_paths[[interval]][[channel]])
+    grobs       <- list()
+    grob_labels <- character(0)
+
+    for (plot_type in plot_types) {
+      plot_name <- plot_type_to_name(plot_type)
+
+      if (multiple_intervals) {
+        ch_id_folder <- file.path(params$base_dir,
+                                  paste0(params$file_id, "_results"),
+                                  "plots", interval, channel)
+      } else {
+        ch_id_folder <- file.path(params$base_dir,
+                                  paste0(params$file_id, "_results"),
+                                  "plots", channel)
+      }
+
+      plot_path <- build_plot_path(file_id      = params$file_id,
+                                   ch_id        = channel,
+                                   ch_id_folder = ch_id_folder,
+                                   plot_name    = plot_name,
+                                   save_format  = params$save_format)
+
+      if (file.exists(plot_path)) {
+        img      <- magick::image_read_svg(plot_path)
+        png_path <- tempfile(fileext = ".png")
+        magick::image_write(img, path = png_path, format = "png", density = 300)
+        grobs[[length(grobs) + 1]] <- grid::rasterGrob(magick::image_read(png_path))
+        grob_labels <- c(grob_labels, plot_type)
+      }
+    }
+
+    n_plots <- length(grobs)
+    if (n_plots > 0) {
+      for (i in seq(1, n_plots, by = 4)) {
+        grid_grobs  <- grobs[i:min(i + 3, n_plots)]
+        grid_labels <- grob_labels[i:min(i + 3, n_plots)]
+
+        if (multiple_intervals) {
+          grid_title <- paste0("Interval: ", interval, " | Plots: ",
+                               paste(grid_labels, collapse = ", "), "\n")
+        } else {
+          grid_title <- paste0("Plots: ", paste(grid_labels, collapse = ", "), "\n")
+        }
+
+        gridExtra::grid.arrange(grobs = grid_grobs, ncol = 2, nrow = 2, top = grid_title)
+        cat("\\newpage\n")
+      }
+    } else {
+      cat("*No plots found for this channel.*\n\n")
+    }
+  }
+
+  if (multiple_intervals) cat("\\newpage\n")
+}
+```
diff --git a/man/generate_file_report.Rd b/man/generate_file_report.Rd
index d55147a..a6346cb 100644
--- a/man/generate_file_report.Rd
+++ b/man/generate_file_report.Rd
@@ -12,8 +12,8 @@ generate_file_report(
   channels,
   plot_types,
   storage_fold = "plots",
-  report_template = "report_template.Rmd",
-  output_dir = file.path(base_dir, "reports")
+  output_dir = file.path(base_dir, "reports"),
+  pdf = FALSE
 )
 }
 \arguments{
@@ -33,14 +33,15 @@ report.}
 \item{storage_fold}{Character; subdirectory containing the plots. Defaults
 to \code{"plots"}.}
 
-\item{report_template}{Character; filename of the Rmd template. Defaults
-to \code{"report_template.Rmd"}.}
-
 \item{output_dir}{Character; directory where the rendered report is saved.
 Defaults to a \code{reports} subdirectory inside \code{base_dir}.}
+
+\item{pdf}{Logical; if \code{TRUE} render a PDF instead of HTML. Requires
+\pkg{magick}, \pkg{tinytex}, and a TinyTeX installation. Defaults to
+\code{FALSE}.}
 }
 \value{
-Called for its side effect of rendering an HTML report; returns
+Called for its side effect of rendering a report; returns
 the output file path invisibly.
 }
 \description{
diff --git a/man/generate_plot_type_reports.Rd b/man/generate_plot_type_reports.Rd
index b5b4e23..9d1bd0e 100644
--- a/man/generate_plot_type_reports.Rd
+++ b/man/generate_plot_type_reports.Rd
@@ -8,8 +8,8 @@ generate_plot_type_reports(
   params,
   file_rows,
   storage_fold = "plots",
-  plot_report_template = "plot_type_report_template.Rmd",
-  plot_report_dir = file.path(params$paths$base_dir, "reports", "plot_reports")
+  plot_report_dir = file.path(params$paths$base_dir, "reports", "plot_reports"),
+  pdf = FALSE
 )
 }
 \arguments{
@@ -21,23 +21,27 @@ generate_plot_type_reports(
 file's results directory where plots are stored. Defaults to
 \code{"plots"}.}
 
-\item{plot_report_template}{Character string giving the filename of the Rmd
-template to use. Defaults to \code{"plot_type_report_template.Rmd"}.}
-
 \item{plot_report_dir}{Character string giving the output directory for
 rendered reports. Defaults to \code{file.path(params$paths$base_dir,
   "reports", "plot_reports")}.}
+
+\item{pdf}{Logical; if \code{TRUE} render PDF reports instead of HTML.
+Requires \pkg{magick}, \pkg{tinytex}, and a TinyTeX installation
+(\code{tinytex::install_tinytex()}). Defaults to \code{FALSE}.}
 }
 \value{
-Called for its side effects (PDF reports written to
+Called for its side effects (reports written to
 \code{plot_report_dir}). Returns \code{NULL} invisibly.
 }
 \description{
-Renders one PDF report per plot type, collating the corresponding plot
-across all files, intervals, and channels using an Rmd template.
+Renders one report per plot type, collating the corresponding plot across
+all files, intervals, and channels using an Rmd template. Output is HTML
+by default; set \code{pdf = TRUE} for PDF output (requires additional
+system dependencies).
 }
 \examples{
 \dontrun{
 generate_plot_type_reports(params, file_rows)
+generate_plot_type_reports(params, file_rows, pdf = TRUE)
 }
 }
diff --git a/man/generate_reports.Rd b/man/generate_reports.Rd
index 7ff0817..394b5c0 100644
--- a/man/generate_reports.Rd
+++ b/man/generate_reports.Rd
@@ -4,23 +4,30 @@
 \alias{generate_reports}
 \title{generate_reports}
 \usage{
-generate_reports(params, file_rows)
+generate_reports(params, file_rows, pdf = FALSE)
 }
 \arguments{
 \item{params}{A named list of analysis parameters as produced by \code{make_params()}.}
 
 \item{file_rows}{A tibble of file metadata as produced by \code{index_files()}.}
+
+\item{pdf}{Logical; if \code{TRUE} render PDF reports instead of HTML.
+Requires \pkg{magick}, \pkg{tinytex}, and a TinyTeX installation
+(\code{tinytex::install_tinytex()}). Defaults to \code{FALSE}.}
 }
 \value{
 Called for its side effects (report files written to disk). Returns
 \code{NULL} invisibly.
 }
 \description{
-Renders a per-file HTML or PDF report for each file in the project,
-collecting all plot types across intervals and channels.
+Renders a per-file report for each file in the project, collecting all
+plot types across intervals and channels. Output is HTML by default;
+set \code{pdf = TRUE} for PDF output (requires additional system
+dependencies).
 }
 \examples{
 \dontrun{
 generate_reports(params, file_rows)
+generate_reports(params, file_rows, pdf = TRUE)
 }
 }
diff --git a/man/pull_plots_old.Rd b/man/pull_plots_old.Rd
deleted file mode 100644
index 36756e1..0000000
--- a/man/pull_plots_old.Rd
+++ /dev/null
@@ -1,55 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils_foo.R
-\name{pull_plots_old}
-\alias{pull_plots_old}
-\title{Copy plots into a subdirectory (deprecated, use \code{pull_plots()})}
-\usage{
-pull_plots_old(
-  base.dir,
-  plot.name,
-  dir.name,
-  file.names,
-  mainfold = FALSE,
-  second_fold = "",
-  channel,
-  storage_fold = "plots",
-  short = FALSE,
-  shortname = "",
-  ...
-)
-}
-\arguments{
-\item{base.dir}{Character; base directory of the project.}
-
-\item{plot.name}{Character; plot filename stem.}
-
-\item{dir.name}{Character; name of the destination subdirectory.}
-
-\item{file.names}{Character vector of file identifiers.}
-
-\item{mainfold}{Logical; if \code{TRUE}, looks for plots directly inside
-each file's results folder. Defaults to \code{FALSE}.}
-
-\item{second_fold}{Character; optional intermediate subdirectory path.
-Defaults to \code{""}.}
-
-\item{channel}{Character; channel identifier used in plot filenames.}
-
-\item{storage_fold}{Character; top-level output folder. Defaults to
-\code{"plots"}.}
-
-\item{short}{Logical; if \code{TRUE}, uses \code{shortname} as the
-destination filename. Defaults to \code{FALSE}.}
-
-\item{shortname}{Character; filename used when \code{short = TRUE}.
-Defaults to \code{""}.}
-
-\item{...}{Currently unused.}
-}
-\value{
-Character vector of destination file paths (invisibly).
-}
-\description{
-Copy plots into a subdirectory (deprecated, use \code{pull_plots()})
-}
-\keyword{internal}