diff --git a/DESCRIPTION b/DESCRIPTION
index aa32e0d..a7414d2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -19,7 +19,6 @@ Imports:
     dagitty (>= 0.3.4),
     DiagrammeR (>= 1.0.11),
     dplyr (>= 1.1.4),
-    messaging (>= 0.1.0),
     purrr (>= 1.1.0),
     rlang (>= 1.1.6),
     stringr (>= 1.5.1),
diff --git a/NAMESPACE b/NAMESPACE
index ba3fbd3..75baf4a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,14 +1,22 @@
 # Generated by roxygen2: do not edit by hand
 
+export(cleanup_existing_theme)
 export(get_conditioned_nodes)
 export(parse_edges)
 export(parse_edgestring)
 export(parse_nodes)
+export(qd_adjustment_sets)
 export(qd_dag)
 export(qd_save)
+export(qd_select_edges)
+export(qd_select_nodes)
+export(qd_set_edge_attrs)
+export(qd_set_node_attrs)
 export(qd_swig)
 export(qd_themes)
 export(qd_todagitty)
+export(select_edges_by_node_alpha_id)
+export(select_nodes_by_alpha_id)
 export(sep_opts)
 export(theme_qd_base)
 export(theme_qd_circles)
diff --git a/R/graph_operations.R b/R/graph_operations.R
new file mode 100644
index 0000000..5e21f8d
--- /dev/null
+++ b/R/graph_operations.R
@@ -0,0 +1,78 @@
+#' Graph operations
+#'
+#' @param graph_obj A `quickdag` object output by [qd_dag()] or [qd_swig()].
+#' @param alpha_ids A vector of alphanumeric node IDs upon which to operate.
+#' @param ... Passed to [DiagrammeR::set_node_attrs()] or [DiagrammeR::set_edge_attrs()]
+#'   argument `node_attr` or `edge_attr`, respectively.
+#'   [DiagrammeR::set_edge_attrs()] argument of the same name.
+#' @param from_alpha A vector of alphanumeric source node IDs.
+#' @param to_alpha A vector of alphanumeric destination node IDs.
+#' @param set_op Passed to the `set_op` argument of [DiagrammeR::select_nodes_by_id()]
+#'   or [DiagrammeR::select_edges_by_node_id()]. Defaults to "union".
+#'
+#' @rdname graph_operations
+#' @export
+qd_set_node_attrs <- function(graph_obj, ..., alpha_ids) {
+  numids <- get_numids(graph_obj, alpha_ids)
+  graph_out <- DiagrammeR::set_node_attrs(graph_obj,
+                                          ...,
+                                          values = values,
+                                          nodes = numids)
+  graph_out
+}
+
+#' @rdname graph_operations
+#' @export
+qd_set_edge_attrs <- function(graph_obj, ...,
+                              from_alpha = NULL, to_alpha = NULL) {
+  from_numids <- NULL
+  to_numids <- NULL
+  if (!is.null(from_alpha)) {
+    from_numids <- get_numids(graph_obj, from_alpha)
+  }
+  if (!is.null(to_alpha)) {
+    to_numids <- get_numids(graph_obj, to_alpha)
+  }
+  graph_out <- DiagrammeR::set_edge_attrs(graph_obj,
+                                          ...,
+                                          values = values,
+                                          from = from_numids,
+                                          to = to_numids)
+  graph_out
+}
+
+#' @rdname graph_operations
+#' @export
+select_nodes_by_alpha_id <- function(graph_obj, alpha_ids, set_op = "union") {
+  numids <- get_numids(graph_obj, alpha_ids)
+  graph_out <- DiagrammeR::select_nodes_by_id(graph_obj,
+                                              nodes = numids,
+                                              set_op = set_op)
+  graph_out
+}
+
+#' @rdname graph_operations
+#' @export
+qd_select_nodes <- select_nodes_by_alpha_id
+
+#' @rdname graph_operations
+#' @export
+select_edges_by_node_alpha_id <- function(graph_obj, alpha_ids, set_op = "union") {
+  numids <- get_numids(graph_obj, alpha_ids)
+  graph_out <- DiagrammeR::select_edges_by_node_id(graph_obj,
+                                                   nodes = numids,
+                                                   set_op = set_op)
+  graph_out
+}
+
+#' @rdname graph_operations
+#' @export
+qd_select_edges <- select_edges_by_node_alpha_id
+
+#' Retrieves numeric IDs given alphanumeric IDs
+#' @inheritParams qd_set_node_attrs
+get_numids <- function(graph_obj, alpha_ids) {
+  graph_obj$nodes_df |>
+    dplyr::filter(alpha_id %in% alpha_ids) |>
+    dplyr::pull(id)
+}
diff --git a/R/parse.R b/R/parse.R
index 116882b..842928d 100644
--- a/R/parse.R
+++ b/R/parse.R
@@ -1,6 +1,6 @@
 #' @title Parse nodes
 #' @inheritParams qd_dag
-#' @rdname node-parsing
+#' @rdname node_parsing
 #' @export
 parse_nodes <- function(edgelist) {
   nodes <- unlist(lapply(edgelist,
@@ -12,7 +12,7 @@ parse_nodes <- function(edgelist) {
 
 #' @title Parse edges in a graph specification
 #' @param edgestring A single string containing some set of node-edge relationships
-#' @rdname edge-parsing
+#' @rdname edge_parsing
 #' @export
 parse_edgestring <- function(edgestring) {
   edgepat <- "\\<\\-\\>|\\-\\>|\\<\\-"
@@ -52,7 +52,7 @@ parse_edgestring <- function(edgestring) {
   Reduce(rbind, edge_mini_dfs)
 }
 
-#' @rdname edge-parsing
+#' @rdname edge_parsing
 #' @inheritParams qd_dag
 #' @export
 parse_edges <- function(edgelist) {
diff --git a/R/qd_dag.R b/R/qd_dag.R
index 9a61e56..caa67ca 100644
--- a/R/qd_dag.R
+++ b/R/qd_dag.R
@@ -11,7 +11,7 @@
 #' @param edge_aes_opts A list feeding aesthetic options for edges to
 #'   [DiagrammeR::edge_aes()]. Defaults to empty list.
 #' @param format_special Render numeric elements in an alphanumeric `alpha_id` as
-#'   subcripts. Defaults to `TRUE`.
+#'   subcripts. Defaults to `FALSE`.
 #' @param verbose Indicate whether to print node and edge dataframes to the console.
 #'   See Details below. Defaults to `TRUE`.
 #' @param check_dag Logical. Check whether the graph conforms to the rules of DAGs.
@@ -31,7 +31,7 @@
 #' edges <- c("A -> { B C } <- L",
 #'            "B -> C")
 #'
-#' # make a DAG object and render the graph using the default theme
+#' # Make a DAG object and render the graph using the default theme
 #' g.obj <- qd_dag(edges)
 #' DiagrammeR::render_graph(g.obj)
 #'
@@ -51,8 +51,11 @@
 #'
 qd_dag <- function(edgelist, node_labs = NULL,
                    node_aes_opts = list(), edge_aes_opts = list(),
-                   format_special = TRUE,
-                   verbose = FALSE, check_dag = TRUE, theme = "base", ...) {
+                   format_special = getOption("quickdag.format_special"),
+                   verbose = getOption("quickdag.verbose"),
+                   check_dag = getOption("quickdag.check_dag"),
+                   theme = getOption("quickdag.theme"),
+                   ...) {
 
   # Identify Nodes --------------------------------------------------------
   ## extract unique nodes, sort in ascending order
@@ -171,5 +174,4 @@ qd_dag <- function(edgelist, node_labs = NULL,
 
   class(graph) <- c("quickdag", "dgr_graph")
   graph
-
 }
diff --git a/R/qd_save.R b/R/qd_save.R
index 6618f29..c8beb7c 100644
--- a/R/qd_save.R
+++ b/R/qd_save.R
@@ -33,7 +33,8 @@
 #'
 #' # clean up temporary directory
 #' file.remove(file)
-qd_save <- function(graph, file_name, ..., embed = FALSE, kg = NULL) {
+qd_save <- function(graph, file_name, ...,
+                    embed = getOption("quickdag.embed"), kg = NULL) {
   DiagrammeR::export_graph(graph = graph, file_name = file_name, ...)
 
   if (embed == TRUE) {
diff --git a/R/qd_swig.R b/R/qd_swig.R
index ecd8b46..7ee1cce 100644
--- a/R/qd_swig.R
+++ b/R/qd_swig.R
@@ -32,8 +32,8 @@
 qd_swig <- function(graph_obj,
                     fixed_nodes,
                     custom_values = NULL,
-                    fixed_sep = "vlin",
-                    sep_point_size = 15) {
+                    fixed_sep = getOption("quickdag.swig_fixedsep"),
+                    sep_point_size = getOption("quickdag.swig_sepsize")) {
 
   ndf <- DiagrammeR::get_node_df(graph_obj)
   ndf$fixed <- with(ndf, ifelse(alpha_id %in% fixed_nodes, TRUE, FALSE))
diff --git a/R/qd_todagitty.R b/R/qd_todagitty.R
index ffa3d76..69b1f06 100644
--- a/R/qd_todagitty.R
+++ b/R/qd_todagitty.R
@@ -3,36 +3,43 @@
 #' @description
 #' Format an edgelist and send it to dagitty to identify variable adjustment sets.
 #'
-#' @param edgelist A vector of edge relationships. Must be strictly organized (see
-#'   example for format).
+#' @param edgelist A vector of edge relationships.
 #' @param diagram_type Character identifying the diagram type. Defaults to "dag", but
-#'   user can specify another graph type (see dagitty documentation).
+#'   user can specify another graph type (see [dagitty::adjustmentSets()]).
 #' @param showplot Logical indicating whether to produce a dagitty plot. Defaults to
 #'   `FALSE`.
 #' @param exposure Character. Specify exposure of interest. (Required)
 #' @param outcome Character. Specifiy outcome of interest. (Required)
-#' @param ... Pass arguments to [dagitty::adjustmentSets()]. See dagitty documentation
-#'   for options.
+#' @param ... Pass arguments to [dagitty::adjustmentSets()].
 #'
 #' @details
-#' The `exposure` and `outcome` options map to dagitty functions of the same name.
+#' The `exposure` and `outcome` options map to dagitty parameters of the same name.
 #'
+#' [qd_todagitty()] remains an alias for [qd_adjustment_sets()] to avoid breaking
+#' existing scripts, as it was the original name of this function.
+#'
+#' @rdname qd_adjustment_sets
 #' @export
 #' @examples
+#' # feed an edgelist to qd_adjustment_sets()
 #' edges <- c("A -> { B C D }",
 #'            "B -> C",
-#'            "E -> { B C }")
-#' # must pass exposure and outcome arguments to dagitty::adjustmentSets()
-#' qd_todagitty(edges, exposure = "A", outcome = "C")
-#' qd_todagitty(edges, exposure = "A", outcome = "C", type = "minimal")
-qd_todagitty <- function(edgelist, diagram_type = "dag", showplot = FALSE,
-                         exposure, outcome,
-                         ...) {
+#'            "E -> { B C }",
+#'            "Y <- L -> A")
+#' qd_adjustment_sets(edges, exposure = "A", outcome = "C")
+#' qd_adjustment_sets(edges, exposure = "A", outcome = "C", type = "minimal")
+#'
+#' # if you've already created a qd_dag() object
+#' dag <- qd_dag(edges)
+#' qd_adjustment_sets(dag$qd_edgelist, exposure = "A", outcome = "Y")
+qd_adjustment_sets <- function(edgelist, diagram_type = "dag", showplot = FALSE,
+                               exposure, outcome,
+                               ...) {
 
-  dagitty_obj <- dagitty::dagitty(paste(diagram_type, "{",
-                                        paste(edgelist, collapse = "; "),
-                                        "}"),
-                                  layout = TRUE)
+  dagitty_obj <- dagitty::dagitty(
+    paste(diagram_type, "{", paste(edgelist, collapse = "; "), "}"),
+    layout = TRUE
+  )
 
   ## optional to show dagitty plot
   if (showplot) {
@@ -40,7 +47,14 @@ qd_todagitty <- function(edgelist, diagram_type = "dag", showplot = FALSE,
   }
 
   ## use dagitty's algorithm to identify adjustment sets
-  sets <- dagitty::adjustmentSets(dagitty_obj, exposure = exposure,
-                                  outcome = outcome, ...)
+  sets <- dagitty::adjustmentSets(dagitty_obj,
+                                  exposure = exposure,
+                                  outcome = outcome,
+                                  ...)
   return(sets)
 }
+
+
+#' @rdname qd_adjustment_sets
+#' @export
+qd_todagitty <- qd_adjustment_sets
diff --git a/R/sep_opts.R b/R/sep_opts.R
index ce3c980..64bb151 100644
--- a/R/sep_opts.R
+++ b/R/sep_opts.R
@@ -40,11 +40,11 @@ sep_opts <- function(entity = NULL, table = FALSE) {
     )
   }
 
-  if (entity %in% names(defopts)) {
+  if (is.null(entity)) {
+    defopts
+  } else if (entity %in% names(defopts)) {
     defopts[names(defopts) == entity]
-  } else if (!is.null(entity)) {
-    entity
   } else {
-    defopts
+    entity
   }
 }
diff --git a/R/themes.R b/R/themes.R
index 3cf5683..29c733b 100644
--- a/R/themes.R
+++ b/R/themes.R
@@ -1,96 +1,168 @@
 #' Diagram themes
 #'
 #' @description
-#' Apply various pre-fabricated themes to diagrams.
+#' Themes and theming utilies.
 #'
 #' @param graph_obj A DAG object created by [qd_dag()].
-#' @param conditioned A character vector indicating which nodes are conditioned upon.
-#'   The shape for these nodes will be set to "square".
 #' @param theme A character string indicating the theme to use. Defaults to "base".
 #'   Set to `NULL` to use GraphViz defaults.
-#' @param font A character vector indicating the font family to use for node labels.
-#'   Defaults to "serif".
-#' @param ... Pass arguments to theme call (e.g., [theme_qd_base()]), such as
-#'   `conditioned` or `font`.
+#' @param conditioned A character vector indicating which nodes are conditioned upon.
+#'   The shape for these nodes will be set to "rectangle".
+#' @param rankdir Direction of node layout. Defaults to "LR", for left-to-right.
+#' @param layout Layout engine. Defaults to "dot", which is the only engine explicitly
+#'   used by [quickdag]. Other options provided by [DiagrammeR] may or may not work
+#'   well.
+#' @param shape Standard node shape for a given graph. Defaults for each theme:
+#'   "base" = plaintex, "circles" = circle, "pearl" = point.
+#'   See [Graphviz documentation](https://graphviz.org/doc/info/shapes.html) for other
+#'   options.
+#' @param arrowhead Shape of the arrowhead. See [DiagrammeR::edge_aes()].
+#' @param arrowsize Size of the arrowhead. See [DiagrammeR::edge_aes()].
+#' @param nodepen Size (in points) of node outlines. By default, controlled
+#'   by package options specific to each theme, each of which defaults to 0.2.
+#' @param nodewidth Width (in inches) of nodes. By default, controlled by package options
+#'   specific to each theme. Defaults to 0.
+#' @param nodeheight Height (in inches) of nodes. By default, controlled by package
+#'   options specific to each theme. Defaults to 0.
+#' @param edgepen Size (in points) of edges. By default, controlled
+#'   by package options specific to each theme, each of which defaults to 0.2.
+#' @param fontname Font name for text elements of the graph. By default, controlled by
+#'   package options specific to each theme, each of which defaults to "Helvetica". This
+#'   is the default in `DiagrammeR`.
+#' @param fontsize Size of text (in points). By default, controlled by package options
+#'   specific to each theme, each of which defaults to 5.
+#' @param fontcolor Text color. By default, controlled by package options
+#'   specific to each theme, each of which defaults to "black".
+#' @param pointsize Size of "point" shape (in points). Applies to "pearl" theme only and
+#'   defaults to 0.02.
+#' @param pointcolor Border color for the "point" shape. Applies to "pearl" theme only
+#'   and defaults to "black".
+#' @param pointfill Fill color for the "point" shape. Applies to "pearl" theme only
+#'   and defaults to "black".
 
 #' @rdname qd_themes
 #' @export
 # wrapper for theme selection
-qd_themes <- function(graph_obj, theme, ...) {
+qd_themes <- function(graph_obj, theme, conditioned = NULL) {
 
   select_theme <- c(
-    "base" = "theme_qd_base",
+    "base"    = "theme_qd_base",
     "circles" = "theme_qd_circles",
-    "pearl" = "theme_qd_pearl"
+    "pearl"   = "theme_qd_pearl"
   )
 
+  if (!theme %in% names(select_theme)) {
+    stop("`theme` must be one of: ", paste(names(select_theme), collapse = ", "))
+  }
+
+  graph_obj <- graph_obj |> cleanup_existing_theme()
+  graph_obj$theme <- theme
+
+  if (!is.null(conditioned)) {
+    graph_obj$conditioned <- conditioned
+  }
+
   do.call(select_theme[theme],
-          args = list(graph_obj = graph_obj, ...))
+          args = list(graph_obj = graph_obj, conditioned = conditioned))
 }
 
 #' @rdname qd_themes
 #' @export
-theme_qd_base <- function(graph_obj, font = "serif", ...) {
-
-  graph_attrs <- tibble::tibble(
-    attr = c("rankdir", "layout"),
-    value = c("LR", "dot"),
-    attr_type = "graph"
-  )
-
-  node_attrs  <- tibble::tibble(
-    attr  = c("shape", "penwidth", "fontname", "width", "height"),
-    value = c("plaintext", "0.5", font, "0", "0"),
-    attr_type = "node"
-  )
-
-  edge_attrs  <- tibble::tibble(
-    attr = c("arrowsize", "penwidth"),
-    value = c("0.4", "0.5"),
-    attr_type = "edge"
-  )
-
-  graph_obj$global_attrs <- dplyr::bind_rows(graph_attrs, node_attrs, edge_attrs)
+theme_qd_base <- function(graph_obj,
+                          rankdir     = getOption("quickdag.base_rankdir"),
+                          layout      = getOption("quickdag.base_layout"),
+                          shape       = getOption("quickdag.base_shape"),
+                          nodepen     = getOption("quickdag.base_nodepen"),
+                          nodewidth   = getOption("quickdag.base_nodewidth"),
+                          nodeheight  = getOption("quickdag.base_nodeheight"),
+                          edgepen     = getOption("quickdag.base_edgepen"),
+                          arrowhead   = getOption("quickdag.base_arrowhead"),
+                          arrowsize   = getOption("quickdag.base_arrowsize"),
+                          fontname    = getOption("quickdag.base_fontname"),
+                          fontsize    = getOption("quickdag.base_fontsize"),
+                          fontcolor   = getOption("quickdag.base_fontcolor"),
+                          conditioned = NULL) {
 
-
-  graph_obj <- graph_obj |> get_conditioned_nodes(...)
+  graph_obj <- graph_obj |>
+    cleanup_existing_theme() |>
+    DiagrammeR::add_global_graph_attrs("rankdir",   "LR", attr_type = "graph") |>
+    DiagrammeR::add_global_graph_attrs("layout",  layout, attr_type = "graph") |>
+    ## Node aesthetics
+    DiagrammeR::set_node_attrs("shape",     shape)      |>
+    DiagrammeR::set_node_attrs("penwidth",  nodepen)    |>
+    DiagrammeR::set_node_attrs("fontname",  fontname)   |>
+    DiagrammeR::set_node_attrs("width",     nodewidth)  |>
+    DiagrammeR::set_node_attrs("height",    nodeheight) |>
+    DiagrammeR::set_node_attrs("headport",  "_")        |>
+    DiagrammeR::set_node_attrs("tailport",  "_")        |>
+    ## Edge aesthetics
+    DiagrammeR::set_edge_attrs("arrowhead", arrowhead)  |>
+    DiagrammeR::set_edge_attrs("arrowsize", arrowsize)  |>
+    DiagrammeR::set_edge_attrs("penwidth",  edgepen)    |>
+    get_conditioned_nodes(conditioned = conditioned)
+
+  graph_obj$theme <- "base"
   graph_obj
 }
 
 #' @rdname qd_themes
 #' @export
-theme_qd_circles <- function(graph_obj, font = "serif", ...) {
-  # set base theme
-  graph_obj <- graph_obj |> theme_qd_base()
+theme_qd_circles <- function(graph_obj,
+                             nodepen     = choose_option("quickdag.circles_nodepen"),
+                             edgepen     = choose_option("quickdag.circles_edgepen"),
+                             fontname    = choose_option("quickdag.circles_fontname"),
+                             fontsize    = choose_option("quickdag.circles_fontsize"),
+                             fontcolor   = choose_option("quickdag.circles_fontcolor"),
+                             conditioned = NULL) {
 
   # tweak base theme
   graph_obj <- graph_obj |>
-    DiagrammeR::add_global_graph_attrs("shape", "circle", "node")
+    theme_qd_base() |>
+    DiagrammeR::add_global_graph_attrs("shape", "circle", "node") |>
+    get_conditioned_nodes(conditioned = conditioned)
 
-  graph_obj <- graph_obj |> get_conditioned_nodes(...)
+  graph_obj$theme <- "circles"
   graph_obj
 }
 
 #' @rdname qd_themes
 #' @export
-theme_qd_pearl <- function(graph_obj, font = "serif", ...) {
-  # set base theme
-  graph_obj <- graph_obj |> theme_qd_base()
-
-  # tweak base theme
+theme_qd_pearl <- function(graph_obj,
+                           pointsize   = getOption("quickdag.pearl_pointsize"),
+                           pointcolor  = getOption("quickdag.pearl_pointcolor"),
+                           pointfill   = getOption("quickdag.pearl_pointfill"),
+                           edgepen     = choose_option("quickdag.pearl_edgepen"),
+                           arrowhead   = choose_option("quickdag.pearl_arrowhead"),
+                           arrowsize   = choose_option("quickdag.pearl_arrowsize"),
+                           fontname    = choose_option("quickdag.pearl_fontname"),
+                           fontsize    = choose_option("quickdag.pearl_fontsize"),
+                           fontcolor   = choose_option("quickdag.pearl_fontcolor"),
+                           conditioned = NULL) {
+
+  # Tweak base theme
   graph_obj <- graph_obj |>
-    # node attribute tweaks
-    DiagrammeR::add_global_graph_attrs("shape", "point", "node") |>
-    DiagrammeR::add_global_graph_attrs("width", 0.2, "node") |>
-    DiagrammeR::add_global_graph_attrs("height", 0.2, "node") |>
-    # edge attribute tweaks
-    DiagrammeR::add_global_graph_attrs("penwidth", 0.2, "edge") |>
-    DiagrammeR::add_global_graph_attrs("arrowsize", 0.2, "edge")
-
-  if (exists("conditioned")) {
-    messaging::emit_message("This theme does not allow for conditioned nodes.")
-  }
-
+    theme_qd_base() |>
+    ## Node attribute tweaks
+    DiagrammeR::set_node_attrs("shape",        "point") |>
+    DiagrammeR::set_node_attrs("style",       "filled") |>
+    DiagrammeR::set_node_attrs("color",     pointcolor) |>
+    DiagrammeR::set_node_attrs("width",      pointsize) |>
+    DiagrammeR::set_node_attrs("height",     pointsize) |>
+    DiagrammeR::set_node_attrs("fixedsize",       TRUE) |>
+    DiagrammeR::set_node_attrs("fontsize",    fontsize) |>
+    ## Add and style external labels
+    DiagrammeR::set_node_attrs("fillcolor", pointfill)  |>
+    DiagrammeR::set_node_attrs("xlabel",    graph_obj$nodes_df$label) |>
+    ## Nuke internal node labels
+    DiagrammeR::set_node_attrs("fontcolor", fontcolor)  |>
+    DiagrammeR::set_node_attrs("label",     "")         |>
+    ## Edge attribute tweaks
+    DiagrammeR::set_edge_attrs("penwidth",     edgepen) |>
+    DiagrammeR::set_edge_attrs("arrowhead",  arrowhead) |>
+    DiagrammeR::set_edge_attrs("arrowsize",  arrowsize) |>
+    get_conditioned_nodes(conditioned = conditioned)
+
+  graph_obj$theme <- "pearl"
   graph_obj
 }
 
@@ -107,16 +179,27 @@ get_conditioned_nodes <- function(graph_obj, conditioned = NULL) {
       DiagrammeR::get_node_ids(conditions = alpha_id %in% conditioned)
 
     graph_obj <- graph_obj |>
-      # add default columns to node_df based on global_attrs
+      ## Add default columns to node_df based on global_attrs
       DiagrammeR::set_node_attrs("shape",  default_shape) |>
       DiagrammeR::set_node_attrs("width",  default_minwd) |>
       DiagrammeR::set_node_attrs("height", default_minht) |>
-      # select conditioned nodes and update node aesthetics
+      ## Select conditioned nodes and update node aesthetics
       DiagrammeR::select_nodes_by_id(cd_nodes) |>
-      DiagrammeR::set_node_attrs_ws("shape",  "square") |>
+      DiagrammeR::set_node_attrs_ws("shape",  "rectangle") |>
       DiagrammeR::set_node_attrs_ws("width",  "0") |>
       DiagrammeR::set_node_attrs_ws("height", "0") |>
       DiagrammeR::clear_selection()
   }
+  graph_obj$conditioned <- conditioned
+  graph_obj
+}
+
+#' @rdname qd_themes
+#' @export
+cleanup_existing_theme <- function(graph_obj) {
+  graph_obj$nodes_df <- graph_obj$nodes_df[, c("id", "type", "label", "alpha_id")]
+  ## Used for the side effect of returning an empty global_attrs table in the
+  ## appropriate format
+  graph_obj$global_attrs <- qd_dag("A", theme = NULL, check_dag = FALSE)$global_attrs
   graph_obj
 }
diff --git a/R/utils.R b/R/utils.R
index 88b12a1..3199998 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1,2 +1,51 @@
 # Put some variables in the global environment to avoid R CMD CHECK notes
-utils::globalVariables(c("alpha_id", "label", "start", "end"))
+utils::globalVariables(c("alpha_id", "label", "start", "end", "id", "values"))
+
+# Set global options
+.onLoad <- function(libname, pkgname) {
+  opts <- list(
+    quickdag.check_dag         = TRUE,
+    quickdag.embed             = FALSE,
+    quickdag.swig_fixedsep     = "vlin",
+    quickdag.swig_sepsize      = 15,
+    quickdag.format_special    = FALSE,
+    quickdag.theme             = "base",
+    quickdag.verbose           = FALSE,
+    quickdag.base_rankdir      = "LR",
+    quickdag.base_layout       = "dot",
+    quickdag.base_nodewidth    = 0,
+    quickdag.base_shape        = "plaintext",
+    quickdag.base_nodepen      = 0.5,
+    quickdag.base_nodeheight   = 0,
+    quickdag.base_edgepen      = 0.5,
+    quickdag.base_arrowhead    = "normal",
+    quickdag.base_arrowsize    = 0.4,
+    quickdag.base_fontname     = "Helvetica", # DiagrammeR's default
+    quickdag.base_fontsize     = 5,
+    quickdag.base_fontcolor    = "black",
+    quickdag.circles_nodepen   = NA,
+    quickdag.circles_edgepen   = NA,
+    quickdag.circles_fontname  = NA,
+    quickdag.circles_fontsize  = NA,
+    quickdag.circles_fontcolor = NA,
+    quickdag.pearl_pointsize   = 0.02,
+    quickdag.pearl_pointcolor  = "black",
+    quickdag.pearl_pointfill   = "black",
+    quickdag.pearl_edgepen     = NA,
+    quickdag.pearl_arrowhead   = NA,
+    quickdag.pearl_arrowsize   = 0.2,
+    quickdag.pearl_fontname    = NA,
+    quickdag.pearl_fontsize    = NA,
+    quickdag.pearl_fontcolor   = NA
+  )
+  options(opts)
+}
+
+choose_option <- function(x) {
+  themeopt <- stringr::str_remove(x, "quickdag\\.(circles|pearl)_")
+  if (is.na(getOption(x))) {
+    getOption(paste0("quickdag.base_", themeopt))
+  } else {
+    getOption(x)
+  }
+}
diff --git a/man/edge-parsing.Rd b/man/edge_parsing.Rd
similarity index 100%
rename from man/edge-parsing.Rd
rename to man/edge_parsing.Rd
diff --git a/man/get_numids.Rd b/man/get_numids.Rd
new file mode 100644
index 0000000..6c77f18
--- /dev/null
+++ b/man/get_numids.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/graph_operations.R
+\name{get_numids}
+\alias{get_numids}
+\title{Retrieves numeric IDs given alphanumeric IDs}
+\usage{
+get_numids(graph_obj, alpha_ids)
+}
+\arguments{
+\item{graph_obj}{A \code{quickdag} object output by \code{\link[=qd_dag]{qd_dag()}} or \code{\link[=qd_swig]{qd_swig()}}.}
+
+\item{alpha_ids}{A vector of alphanumeric node IDs upon which to operate.}
+}
+\description{
+Retrieves numeric IDs given alphanumeric IDs
+}
diff --git a/man/graph_operations.Rd b/man/graph_operations.Rd
new file mode 100644
index 0000000..da5cc47
--- /dev/null
+++ b/man/graph_operations.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/graph_operations.R
+\name{qd_set_node_attrs}
+\alias{qd_set_node_attrs}
+\alias{qd_set_edge_attrs}
+\alias{select_nodes_by_alpha_id}
+\alias{qd_select_nodes}
+\alias{select_edges_by_node_alpha_id}
+\alias{qd_select_edges}
+\title{Graph operations}
+\usage{
+qd_set_node_attrs(graph_obj, ..., alpha_ids)
+
+qd_set_edge_attrs(graph_obj, ..., from_alpha = NULL, to_alpha = NULL)
+
+select_nodes_by_alpha_id(graph_obj, alpha_ids, set_op = "union")
+
+qd_select_nodes(graph_obj, alpha_ids, set_op = "union")
+
+select_edges_by_node_alpha_id(graph_obj, alpha_ids, set_op = "union")
+
+qd_select_edges(graph_obj, alpha_ids, set_op = "union")
+}
+\arguments{
+\item{graph_obj}{A \code{quickdag} object output by \code{\link[=qd_dag]{qd_dag()}} or \code{\link[=qd_swig]{qd_swig()}}.}
+
+\item{...}{Passed to \code{\link[DiagrammeR:set_node_attrs]{DiagrammeR::set_node_attrs()}} or \code{\link[DiagrammeR:set_edge_attrs]{DiagrammeR::set_edge_attrs()}}
+argument \code{node_attr} or \code{edge_attr}, respectively.
+\code{\link[DiagrammeR:set_edge_attrs]{DiagrammeR::set_edge_attrs()}} argument of the same name.}
+
+\item{alpha_ids}{A vector of alphanumeric node IDs upon which to operate.}
+
+\item{from_alpha}{A vector of alphanumeric source node IDs.}
+
+\item{to_alpha}{A vector of alphanumeric destination node IDs.}
+
+\item{set_op}{Passed to the \code{set_op} argument of \code{\link[DiagrammeR:select_nodes_by_id]{DiagrammeR::select_nodes_by_id()}}
+or \code{\link[DiagrammeR:select_edges_by_node_id]{DiagrammeR::select_edges_by_node_id()}}. Defaults to "union".}
+}
+\description{
+Graph operations
+}
diff --git a/man/node-parsing.Rd b/man/node_parsing.Rd
similarity index 100%
rename from man/node-parsing.Rd
rename to man/node_parsing.Rd
diff --git a/man/qd_adjustment_sets.Rd b/man/qd_adjustment_sets.Rd
new file mode 100644
index 0000000..d0ff60a
--- /dev/null
+++ b/man/qd_adjustment_sets.Rd
@@ -0,0 +1,62 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/qd_todagitty.R
+\name{qd_adjustment_sets}
+\alias{qd_adjustment_sets}
+\alias{qd_todagitty}
+\title{Identify variables for adjustment}
+\usage{
+qd_adjustment_sets(
+  edgelist,
+  diagram_type = "dag",
+  showplot = FALSE,
+  exposure,
+  outcome,
+  ...
+)
+
+qd_todagitty(
+  edgelist,
+  diagram_type = "dag",
+  showplot = FALSE,
+  exposure,
+  outcome,
+  ...
+)
+}
+\arguments{
+\item{edgelist}{A vector of edge relationships.}
+
+\item{diagram_type}{Character identifying the diagram type. Defaults to "dag", but
+user can specify another graph type (see \code{\link[dagitty:adjustmentSets]{dagitty::adjustmentSets()}}).}
+
+\item{showplot}{Logical indicating whether to produce a dagitty plot. Defaults to
+\code{FALSE}.}
+
+\item{exposure}{Character. Specify exposure of interest. (Required)}
+
+\item{outcome}{Character. Specifiy outcome of interest. (Required)}
+
+\item{...}{Pass arguments to \code{\link[dagitty:adjustmentSets]{dagitty::adjustmentSets()}}.}
+}
+\description{
+Format an edgelist and send it to dagitty to identify variable adjustment sets.
+}
+\details{
+The \code{exposure} and \code{outcome} options map to dagitty parameters of the same name.
+
+\code{\link[=qd_todagitty]{qd_todagitty()}} remains an alias for \code{\link[=qd_adjustment_sets]{qd_adjustment_sets()}} to avoid breaking
+existing scripts, as it was the original name of this function.
+}
+\examples{
+# feed an edgelist to qd_adjustment_sets()
+edges <- c("A -> { B C D }",
+           "B -> C",
+           "E -> { B C }",
+           "Y <- L -> A")
+qd_adjustment_sets(edges, exposure = "A", outcome = "C")
+qd_adjustment_sets(edges, exposure = "A", outcome = "C", type = "minimal")
+
+# if you've already created a qd_dag() object
+dag <- qd_dag(edges)
+qd_adjustment_sets(dag$qd_edgelist, exposure = "A", outcome = "Y")
+}
diff --git a/man/qd_dag.Rd b/man/qd_dag.Rd
index f930617..56c6f88 100644
--- a/man/qd_dag.Rd
+++ b/man/qd_dag.Rd
@@ -9,10 +9,10 @@ qd_dag(
   node_labs = NULL,
   node_aes_opts = list(),
   edge_aes_opts = list(),
-  format_special = TRUE,
-  verbose = FALSE,
-  check_dag = TRUE,
-  theme = "base",
+  format_special = getOption("quickdag.format_special"),
+  verbose = getOption("quickdag.verbose"),
+  check_dag = getOption("quickdag.check_dag"),
+  theme = getOption("quickdag.theme"),
   ...
 )
 }
@@ -29,7 +29,7 @@ to \code{NULL}.}
 \code{\link[DiagrammeR:edge_aes]{DiagrammeR::edge_aes()}}. Defaults to empty list.}
 
 \item{format_special}{Render numeric elements in an alphanumeric \code{alpha_id} as
-subcripts. Defaults to \code{TRUE}.}
+subcripts. Defaults to \code{FALSE}.}
 
 \item{verbose}{Indicate whether to print node and edge dataframes to the console.
 See Details below. Defaults to \code{TRUE}.}
@@ -56,7 +56,7 @@ the same letter as their corresponding \code{alpha_id}, which may not always be
 edges <- c("A -> { B C } <- L",
            "B -> C")
 
-# make a DAG object and render the graph using the default theme
+# Make a DAG object and render the graph using the default theme
 g.obj <- qd_dag(edges)
 DiagrammeR::render_graph(g.obj)
 
diff --git a/man/qd_save.Rd b/man/qd_save.Rd
index 0285083..33b69cd 100644
--- a/man/qd_save.Rd
+++ b/man/qd_save.Rd
@@ -4,7 +4,7 @@
 \alias{qd_save}
 \title{Save graph objects as images}
 \usage{
-qd_save(graph, file_name, ..., embed = FALSE, kg = NULL)
+qd_save(graph, file_name, ..., embed = getOption("quickdag.embed"), kg = NULL)
 }
 \arguments{
 \item{graph}{A graph object produced by \code{\link[=qd_dag]{qd_dag()}}}
diff --git a/man/qd_swig.Rd b/man/qd_swig.Rd
index 9fb49b2..767fb04 100644
--- a/man/qd_swig.Rd
+++ b/man/qd_swig.Rd
@@ -8,8 +8,8 @@ qd_swig(
   graph_obj,
   fixed_nodes,
   custom_values = NULL,
-  fixed_sep = "vlin",
-  sep_point_size = 15
+  fixed_sep = getOption("quickdag.swig_fixedsep"),
+  sep_point_size = getOption("quickdag.swig_sepsize")
 )
 }
 \arguments{
diff --git a/man/qd_themes.Rd b/man/qd_themes.Rd
index e06afe0..6f298c6 100644
--- a/man/qd_themes.Rd
+++ b/man/qd_themes.Rd
@@ -6,17 +6,55 @@
 \alias{theme_qd_circles}
 \alias{theme_qd_pearl}
 \alias{get_conditioned_nodes}
+\alias{cleanup_existing_theme}
 \title{Diagram themes}
 \usage{
-qd_themes(graph_obj, theme, ...)
+qd_themes(graph_obj, theme, conditioned = NULL)
 
-theme_qd_base(graph_obj, font = "serif", ...)
+theme_qd_base(
+  graph_obj,
+  rankdir = getOption("quickdag.base_rankdir"),
+  layout = getOption("quickdag.base_layout"),
+  shape = getOption("quickdag.base_shape"),
+  nodepen = getOption("quickdag.base_nodepen"),
+  nodewidth = getOption("quickdag.base_nodewidth"),
+  nodeheight = getOption("quickdag.base_nodeheight"),
+  edgepen = getOption("quickdag.base_edgepen"),
+  arrowhead = getOption("quickdag.base_arrowhead"),
+  arrowsize = getOption("quickdag.base_arrowsize"),
+  fontname = getOption("quickdag.base_fontname"),
+  fontsize = getOption("quickdag.base_fontsize"),
+  fontcolor = getOption("quickdag.base_fontcolor"),
+  conditioned = NULL
+)
 
-theme_qd_circles(graph_obj, font = "serif", ...)
+theme_qd_circles(
+  graph_obj,
+  nodepen = choose_option("quickdag.circles_nodepen"),
+  edgepen = choose_option("quickdag.circles_edgepen"),
+  fontname = choose_option("quickdag.circles_fontname"),
+  fontsize = choose_option("quickdag.circles_fontsize"),
+  fontcolor = choose_option("quickdag.circles_fontcolor"),
+  conditioned = NULL
+)
 
-theme_qd_pearl(graph_obj, font = "serif", ...)
+theme_qd_pearl(
+  graph_obj,
+  pointsize = getOption("quickdag.pearl_pointsize"),
+  pointcolor = getOption("quickdag.pearl_pointcolor"),
+  pointfill = getOption("quickdag.pearl_pointfill"),
+  edgepen = choose_option("quickdag.pearl_edgepen"),
+  arrowhead = choose_option("quickdag.pearl_arrowhead"),
+  arrowsize = choose_option("quickdag.pearl_arrowsize"),
+  fontname = choose_option("quickdag.pearl_fontname"),
+  fontsize = choose_option("quickdag.pearl_fontsize"),
+  fontcolor = choose_option("quickdag.pearl_fontcolor"),
+  conditioned = NULL
+)
 
 get_conditioned_nodes(graph_obj, conditioned = NULL)
+
+cleanup_existing_theme(graph_obj)
 }
 \arguments{
 \item{graph_obj}{A DAG object created by \code{\link[=qd_dag]{qd_dag()}}.}
@@ -24,15 +62,55 @@ get_conditioned_nodes(graph_obj, conditioned = NULL)
 \item{theme}{A character string indicating the theme to use. Defaults to "base".
 Set to \code{NULL} to use GraphViz defaults.}
 
-\item{...}{Pass arguments to theme call (e.g., \code{\link[=theme_qd_base]{theme_qd_base()}}), such as
-\code{conditioned} or \code{font}.}
+\item{conditioned}{A character vector indicating which nodes are conditioned upon.
+The shape for these nodes will be set to "rectangle".}
+
+\item{rankdir}{Direction of node layout. Defaults to "LR", for left-to-right.}
 
-\item{font}{A character vector indicating the font family to use for node labels.
-Defaults to "serif".}
+\item{layout}{Layout engine. Defaults to "dot", which is the only engine explicitly
+used by \link{quickdag}. Other options provided by \link[DiagrammeR:DiagrammeR]{DiagrammeR::DiagrammeR} may or may not work
+well.}
 
-\item{conditioned}{A character vector indicating which nodes are conditioned upon.
-The shape for these nodes will be set to "square".}
+\item{shape}{Standard node shape for a given graph. Defaults for each theme:
+"base" = plaintex, "circles" = circle, "pearl" = point.
+See \href{https://graphviz.org/doc/info/shapes.html}{Graphviz documentation} for other
+options.}
+
+\item{nodepen}{Size (in points) of node outlines. By default, controlled
+by package options specific to each theme, each of which defaults to 0.2.}
+
+\item{nodewidth}{Width (in inches) of nodes. By default, controlled by package options
+specific to each theme. Defaults to 0.}
+
+\item{nodeheight}{Height (in inches) of nodes. By default, controlled by package
+options specific to each theme. Defaults to 0.}
+
+\item{edgepen}{Size (in points) of edges. By default, controlled
+by package options specific to each theme, each of which defaults to 0.2.}
+
+\item{arrowhead}{Shape of the arrowhead. See \code{\link[DiagrammeR:edge_aes]{DiagrammeR::edge_aes()}}.}
+
+\item{arrowsize}{Size of the arrowhead. See \code{\link[DiagrammeR:edge_aes]{DiagrammeR::edge_aes()}}.}
+
+\item{fontname}{Font name for text elements of the graph. By default, controlled by
+package options specific to each theme, each of which defaults to "Helvetica". This
+is the default in \code{DiagrammeR}.}
+
+\item{fontsize}{Size of text (in points). By default, controlled by package options
+specific to each theme, each of which defaults to 5.}
+
+\item{fontcolor}{Text color. By default, controlled by package options
+specific to each theme, each of which defaults to "black".}
+
+\item{pointsize}{Size of "point" shape (in points). Applies to "pearl" theme only and
+defaults to 0.02.}
+
+\item{pointcolor}{Border color for the "point" shape. Applies to "pearl" theme only
+and defaults to "black".}
+
+\item{pointfill}{Fill color for the "point" shape. Applies to "pearl" theme only
+and defaults to "black".}
 }
 \description{
-Apply various pre-fabricated themes to diagrams.
+Themes and theming utilies.
 }
diff --git a/man/qd_todagitty.Rd b/man/qd_todagitty.Rd
deleted file mode 100644
index 50350fd..0000000
--- a/man/qd_todagitty.Rd
+++ /dev/null
@@ -1,46 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/qd_todagitty.R
-\name{qd_todagitty}
-\alias{qd_todagitty}
-\title{Identify variables for adjustment}
-\usage{
-qd_todagitty(
-  edgelist,
-  diagram_type = "dag",
-  showplot = FALSE,
-  exposure,
-  outcome,
-  ...
-)
-}
-\arguments{
-\item{edgelist}{A vector of edge relationships. Must be strictly organized (see
-example for format).}
-
-\item{diagram_type}{Character identifying the diagram type. Defaults to "dag", but
-user can specify another graph type (see dagitty documentation).}
-
-\item{showplot}{Logical indicating whether to produce a dagitty plot. Defaults to
-\code{FALSE}.}
-
-\item{exposure}{Character. Specify exposure of interest. (Required)}
-
-\item{outcome}{Character. Specifiy outcome of interest. (Required)}
-
-\item{...}{Pass arguments to \code{\link[dagitty:adjustmentSets]{dagitty::adjustmentSets()}}. See dagitty documentation
-for options.}
-}
-\description{
-Format an edgelist and send it to dagitty to identify variable adjustment sets.
-}
-\details{
-The \code{exposure} and \code{outcome} options map to dagitty functions of the same name.
-}
-\examples{
-edges <- c("A -> { B C D }",
-           "B -> C",
-           "E -> { B C }")
-# must pass exposure and outcome arguments to dagitty::adjustmentSets()
-qd_todagitty(edges, exposure = "A", outcome = "C")
-qd_todagitty(edges, exposure = "A", outcome = "C", type = "minimal")
-}