BodyMapR - An R Package and Shiny Application Designed to Generate Anatomical Visualizations of Cancer Lesions

Publication
Preprint
Article and Authorship Details

Article type: This is a pre-print. This article is currently under review.

Authors: David M. Miller1* MD PhD, Sophia Z. Shalhout1 PhD

1Department of Medicine, Division of Hematology/Oncology and the Department of Dermatology, Massachusetts General Hospital, Boston, MA

*Corresponding author: David M. Miller MD PhD
Massachusetts General Hospital
15 Parkman St. Room 132
Boston MA 02114
Telephone: 617-726-2667
Fax: 617-643-1740
Email:

Funding sources: The Harvard Cancer Center Merkel Cell Carcinoma patient registry is supported by grants from Project Data Sphere, the American Skin Association and ECOG-ACRIN.

Conflicts of interest: None

Manuscript word count: 1910 [max 2000 excluding abstract/tabs/figs/res/suppl]
Abstract word count: 149 [max 150]
References: 22 [unlimited]
Figures: 8 [max 3]
Tables: 5 [max 2]

Keywords: data visualization, cancer, shiny app, REDCap

Acknowledgments:

Abbreviations: CSV: comma-separated values, CTC: clinical tumor characteristics, GLP: geographical lesion profile, ICD-O-3: International Classification of Diseases for Oncology, 3rd edition, IDE: integrated development environment, MCC: merkel cell carcinoma, RWD: real-world data, REDCap: Research Electronic Data Capture, SNOMED: Systematized Nomenclature of Medicine, UI: user interface.

ABSTRACT

Objectives: Structured real-world data, such as those found in cancer registries, provide a rich source of information regarding the natural history of cancer. Interactive data visualizations of cancer lesions can provide insights into certain clinical tumor characteristics. Software that can be integrated into an oncological data collection effort and generate anatomical data visualizations of clinical tumor characteristics are limited.
Materials and Methods: We created BodyMapR: an R package and Shiny application that generates anatomical visualizations of cancer lesions from structured data.
Results: BodyMapR is a shiny application that transposes structured data from REDCap® onto an anatomical map to yield an interactive data visualization.
Conclusions: BodyMapR is freely available under the MIT license and can be obtained from GitHub. BodyMapR is executed in R and deployed as a Shiny application. It can be integrated into an existing cancer research platform and produces an interactive data visualization of clinical tumor characteristics.

OBJECTIVES

Large-scale data collection efforts in rare cancers, such as Merkel Cell Carcinoma (MCC), are challenging and uncommon1. The dearth of structured data have limited our understanding of the natural history of rare cancers, such as MCC2,3. Consequently, we lack a comprehensive understanding of clinical tumor characteristics (CTC), such as patterns of metastatic spread and biomarkers predictive of treatment response, for most rare tumors. Data collection efforts that incorporate structured data captured during real-world practice (a.k.a Real-World Data or RWD) can improve our understanding of CTC.

Depicting RWD, e.g. from a cancer registry, onto graphical representations of anatomical structures can provide a user-friendly technique to process information regarding CTC. However, displaying large amounts of RWD onto anatomical data visualizations is labor-intensive and time consuming. While informatic packages that generate modular visualizations of anatograms and tissues are available4, software that fully integrates data collection instruments for real-time anatomical data visualizations of cancer registry data are lacking.

We previously published an overview of a methodology and design of a Research Electronic Data Capture (REDCap®)5-based system to facilitate capture of RWD6,1. That platform incorporates a form entitled the Lesion Information instrument, which provides a structured format for the collection of CTC7. This instrument is freely available and can be incorporated into any existing REDCap project. It is currently being used by the Project Data Sphere led Merkel Cell Carcinoma Patient Registry1.

Here we present BodyMapR, an R package with a Shiny application front-end, which generates an interactive data visualization of CTC. Its software wrangles and transforms structured data from a REDCap® project and provides graphing functions (Figure 1). BodyMapR is executed in R but is deployed as a Shiny application to enhance the user interface for users with limited programming capabilities. In this manuscript we provide (1) instructions on how to obtain and execute BodyMapR, (2) the R code for the server side functions to allow for project-specific adaptations, (3) a Biorender-generated png file in which data is overlaid and displayed, and (4) a sample dataset for demonstration purposes.

Figure 1. Schema of BodyMapR

Figure 1. Schema of BodyMapR. BodyMapR takes data from a REDCap® project that incorporates the Lesion Information and Genonimcs instruments. This csv file is loaded into the Shiny application and end users engage BodyMapR via a browser-based interface. Server side R code executes the functions of BodyMapR to generate an interactive Plotly visualization of clinical tumor characteristic data displayed onto an anatomical body map. Anatomical images created with BioRender.com.

METHODS

Software Dependencies

BodyMapR is written in R (version 4.0.0), organized using roxygen28, and utilizes the following packages dplyr9, tidyr10, readr11, stringr12, purrr13, magrittr14, plotly15, shinydashboard16 and Shiny17. For full details, instructions and examples refer to the video demonstration, or README file, both of which can be viewed on the package GitHub page.

Clinical Informatics Dependencies

BodyMapR facilitates data visualizations from structured data contained in the Lesion Information instrument stored within REDCap® project. The data dictionary for this form has been previously published18. BodyMapR also integrates clinico-genomic data from the Genomics data capture instrument, which has been previously described6,19 and is freely available on GitHub(https://github.com/TheMillerLab/genetex/blob/main/data-raw/genomics_data_dictionary.csv).

RESULTS

BodyMapR Inputs

As depicted in Figure 1, BodyMapR takes data from a REDCap® project that has incorporated the Lesion Information and Genomics instruments as the input. The BodyMapR Shiny application is launched via the function launch_BodyMapR(). This function takes one argument, “Data”, a raw csv file exported from REDCap®. launch_BodyMapR() is the only function an end user needs to call to execute and utilize BodyMapR. Once launched, clinical researchers interface with BodyMapR in a web browser. The application’s browser-based user interface (UI) facilitates its use by investigators with limited programming skills. launch_BodyMapR() has a built-in default data set “BodyMapR_mock_dataset”. If the argument “Data” is not specified by an end user, the default data set will be incorporated into the application for demonstration purposes. “BodyMapR_mock_dataset” is a synthetic data set and contains no protected health information.

BodyMapR UI

The centerpiece of the BodyMapR UI is an anatomical landscape, henceforth referred to as the “Body Map” (Figure 2).
Figure 2: Browser-Based User Interface


Figure 2: Browser-Based User Interface. Users control what input is displayed onto the BodyMapR anatomical graphic using the sidebar selectors. Anatomical images created with BioRender.com.

The Body Map includes a skeleton, the anterior and posterior likeness of an androgynous adult, and representations of visceral and lymphatic structures. We designed the Body Map using images from BioRender.com20. Users control what information is displayed onto the Body Map via the application’s UI sidebar. Given that an improved understanding of the geographical lesion profile (GLP) of a cancer type may provide insight into patterns of spread, the default settings of BodyMapR display the GLP of the entire cohort, color-coded by tumor morphology (e.g. primary vs. metastasis vs. recurrence). In contrast, a personalized Body Map at the single-subject level can be obtained by selecting a Record ID from the selectizeInput() selector “Filter on Record ID” in the application’s sidebar (Figure 3).

Figure 3: Data visualization of clinlical tumor characteristics


Figure 3: Data visualization of clinlical tumor characteristics. Depicted is the output of BodyMapR following selection of a specific subject, “Record ID 1”. Anatomical images created with BioRender.com.

Although cancer types have been historically grouped based on the tissue of origin (e.g. “lung cancer” or “pancreatic cancer”), neoplasms originating from the same tissue can have clinically-relevant distinctions in pathogenesis. For example, in Merkel cell carcinoma, at least two distinct transforming mechanisms (e.g. the Merkel cell polyoma virus and ultraviolet radiation), with distinct underlying mutational landscapes, have been described2. Data demonstrating geographical differences in virus-positive vs. virus-negative MCC has emerged21. Thus, further definition of the relationship between topography and mutational landscape may lead to insights in pathogenesis across cancer types. Therefore, BodyMapR incorporates the Genomics Instruments in order to display over 900 genes found in common clinico-genomics platforms6. Users can select which genes to be visualized on the Body Map using “Filter on Gene Mutations” selector (Figure 2).

BodyMapR Server Side Functions

The server side of the Shiny application contains the executable code of BodyMapR. The package contains, in addition to launch_BodyMapR(), a set of functions that wrangles, transforms and graphs CTC data from a REDCap® project (Figure 1). Table 1 summarizes the package’s functions and their respective action.
Table 1 - BodyMapR Functions
Functions Function
bodymapr_df() Creates a data frame of clinical tumor characteristics from a structured electronic data collection instrument (e.g. the Lesion Information instrument) and maps them to lookup tables that contain a coordinate system for the Body Map
bodymapr_plot() Creates an interactive data visualization of clinical tumor characteristics from a structured EDC lesion instrument that has been processed by bodymapr_df().
genomics.df.unite() Wrangles and processes genomics data from a REDCap project that has incorporated the Genomics Instrument. Genetic alterations are listed in wide format with a concatenation of genomic alterations in one cell. This function is called within BodyMapR’s bodymapr_df() function.
genomics.df.long() Wrangles and processes genomics data from a REDCap project that has incorporated the Genomics Instrument. This allows for expedited analysis of patient-level data from REDCap. Genetic alterations are listed in long format. This function is called within BodyMapR’s genomics.df.unite() function.
shiny_server() Contains the server side of the shiny application. It incorporates both bodymapr_df() and bodymapr_plot(). Therefore, the data is wrangled, processed and graphed with this function.
shiny_ui() Creates the user interface of BodyMapR.
launch_BodyMapR() Launches the BodyMapR shiny application.
Table 1 - BodyMapR Functions. Key functions unique to BodyMapR with a brief description of their action are shown.

BodyMapR Outputs

Topographical Mapping

As described previously18, the Lesion Information instrument was designed to capture 651 distinct anatomical structures, including skeletal, cutaneous, lymphatic, mucosal and visceral locations (Table 2).
Table 2: Anatomical Structures
Anatomic Structure
Anterior Medial Left Abdomen Skin
Anterior Midline Left Abdomen Skin
Anterior Lateral Left Abdomen Skin
Left Abdominal Lymphoid Tissue
Left Adenoid Lymphoid Tissue
Left Adrenal
Anterior Medial Left Ankle Skin
Anterior Midline Left Ankle Skin
Anterior Lateral Left Ankle Skin
Posterior Lateral Left Ankle Skin
Posterior Midline Left Ankle Skin
Posterior Medial Left Ankle Skin
Left Axillary Lymphoid Tissue
Posterior Lateral Left Back Skin
Midline Left Back Skin
Posterior Medial Left Back Skin
Medial Left Back Skin
Left Bladder
Left Brachial Lymphoid Tissue
Posterior Lateral Left Buttocks Skin
Midline Left Buttocks Skin
Posterior Medial Left Buttocks Skin
Left Buttocks Skin
Medial Left Buttocks Skin
Left Calcaneus Bone
Left Capitate Bone
Left Celiac Lymphoid Tissue
Anterior Medial Left Cheek Skin
Anterior Midline Left Cheek Skin
Anterior Lateral Left Cheek Skin
Anterior Medial Left Chest Skin
Anterior Midline Left Chest Skin
Anterior Lateral Left Chest Skin
Anterior Medial Left Chin Skin
Anterior Midline Left Chin Skin
Anterior Lateral Left Chin Skin
Left Clavicle Or Collarbone Bone
Left Cuboid Bone
Anterior Medial Left Ear Skin
Anterior Lateral Left Ear Skin
Posterior Medial Left Ear Skin
Posterior Lateral Left Ear Skin
Posterior Midline Left Ear Skin
Anterior Medial Left Elbow Skin
Anterior Midline Left Elbow Skin
Anterior Lateral Left Elbow Skin
Posterior Lateral Left Elbow Skin
Posterior Midline Left Elbow Skin
Posterior Medial Left Elbow Skin
Left Epitrochlear Lymphoid Tissue
Left Ethmoid Bone
Anterior Medial Left Eyebrow Skin
Anterior Midline Left Eyebrow Skin
Anterior Lateral Left Eyebrow Skin
Anterior Medial Left Eyelid Skin
Anterior Midline Left Eyelid Skin
Anterior Lateral Left Eyelid Skin
Left Femoral Lymphoid Tissue
Left Femur Bone
Left Fibula Bone
Anterior Medial Left Foot And Toes Skin
Anterior Midline Left Foot And Toes Skin
Anterior Lateral Left Foot And Toes Skin
Posterior Lateral Left Foot And Toes Skin
Posterior Midline Left Foot And Toes Skin
Left Foot Distal Phalange 1 Bone
Left Foot Distal Phalange 2 Bone
Left Foot Distal Phalange 3 Bone
Left Foot Distal Phalange 4 Bone
Left Foot Distal Phalange 5 Bone
Left Foot Middle Phalange 2 Bone
Left Foot Middle Phalange 3 Bone
Left Foot Middle Phalange 4 Bone
Left Foot Middle Phalange 5 Bone
Left Foot Proximal Phalange 1 Bone
Left Foot Proximal Phalange 2 Bone
Left Foot Proximal Phalange 3 Bone
Left Foot Proximal Phalange 4 Bone
Left Foot Proximal Phalange 5 Bone
Anterior Medial Left Forearm Skin
Anterior Midline Left Forearm Skin
Anterior Lateral Left Forearm Skin
Posterior Lateral Left Forearm Skin
Posterior Midline Left Forearm Skin
Posterior Medial Left Forearm Skin
Anterior Medial Left Forehead Skin
Anterior Midline Left Forehead Skin
Lateral Left Forehead Skin
Anterior Lateral Left Forehead Skin
Left Frontal Bone
Left Gallbladder
Anterior Medial Left Genitalia Skin
Anterior Midline Left Genitalia Skin
Midline Left Genitalia Skin
Posterior Lateral Left Genitalia Skin
Posterior Midline Left Genitalia Skin
Posterior Medial Left Genitalia Skin
Left Hamate Bone
Anterior Medial Left Hand And Fingers Skin
Anterior Midline Left Hand And Fingers Skin
Anterior Lateral Left Hand And Fingers Skin
Posterior Lateral Left Hand And Fingers Skin
Posterior Midline Left Hand And Fingers Skin
Posterior Medial Left Hand And Fingers Skin
Left Hand Distal Phalange 1 Bone
Left Hand Distal Phalange 2 Bone
Left Hand Distal Phalange 3 Bone
Left Hand Distal Phalange 4 Bone
Left Hand Distal Phalange 5 Bone
Left Hand Middle Phalange 2 Bone
Left Hand Middle Phalange 3 Bone
Left Hand Middle Phalange 4 Bone
Left Hand Middle Phalange 5 Bone
Left Hand Proximal Phalange 1 Bone
Left Hand Proximal Phalange 2 Bone
Left Hand Proximal Phalange 3 Bone
Left Hand Proximal Phalange 4 Bone
Left Hand Proximal Phalange 5 Bone
Left Heart
Left Hilar Lymphoid Tissue
Left Humerus Bone
Left Iliac Lymphoid Tissue
Left Ilium Bone
Left Incus Bone
Left Inferior Nasal Conchae Bone
Left Infraclavicular Lymphoid Tissue
Left Inguinal Lymphoid Tissue
Left Intermediate Cuneiform Bone
Left Ischium Bone
Left Kidney
Anterior Medial Left Knee Skin
Anterior Midline Left Knee Skin
Anterior Lateral Left Knee Skin
Posterior Lateral Left Knee Skin
Posterior Midline Left Knee Skin
Posterior Medial Left Knee Skin
Left Lacrimal Bone
Left Large Intestine
Left Lateral Cuneiform Bone
Left Level Ii Cervical Lymphoid Tissue
Left Level Iii Cervical Lymphoid Tissue
Left Level Iv Cervical Lymphoid Tissue
Left Level V Cervical Lymphoid Tissue
Left Level Vi Cervical Lymphoid Tissue
Left Level Vii Cervical Lymphoid Tissue
Left Lingual Tonsils Lymphoid Tissue
Anterior Medial Left Lip Skin
Anterior Lateral Left Lip Skin
Anterior Midline Left Lip Skin
Left Liver
Anterior Medial Left Lower Leg (Shin And Calf) Skin
Anterior Midline Left Lower Leg (Shin And Calf) Skin
Anterior Lateral Left Lower Leg (Shin And Calf) Skin
Posterior Lateral Left Lower Leg (Shin And Calf) Skin
Posterior Midline Left Lower Leg (Shin And Calf) Skin
Posterior Medial Left Lower Leg (Shin And Calf) Skin
Left Lunate Bone
Left Lungs
Left Malleus Bone
Left Mandible Bone
Left Maxilla Bone
Left Medial Cuneiform Bone
Left Mesenteric Lymphoid Tissue
Left Metacarpal 1 Bone
Left Metacarpal 2 Bone
Left Metacarpal 3 Bone
Left Metacarpal 4 Bone
Left Metacarpal 5 Bone
Left Metatarsal 1 Bone
Left Metatarsal 2 Bone
Left Metatarsal 3 Bone
Left Metatarsal 4 Bone
Left Metatarsal 5 Bone
Left Nasal Bone
Left Nasopharynx Lymphoid Tissue
Left Navicular Bone
Anterior Medial Left Neck Skin
Anterior Midline Left Neck Skin
Anterior Lateral Left Neck Skin
Posterior Lateral Left Neck Skin
Posterior Midline Left Neck Skin
Posterior Medial Left Neck Skin
Anterior Medial Left Nose Skin
Anterior Midline Left Nose Skin
Anterior Lateral Left Nose Skin
Left Occipital Lymphoid Tissue
Left Occipital Bone
Left Ossa Coxae Bone
Left Ovary
Left Palatine Bone
Left Pancreas
Left Paraaortic Lymphoid Tissue
Left Parietal Bone
Left Parotid Lymphoid Tissue
Left Patella Bone
Left Pectoral Lymphoid Tissue
Left Peritracheal Lymphoid Tissue
Left Pisiform Bone
Left Popliteal Lymphoid Tissue
Left Porta Hepatis Lymphoid Tissue
Left Preauricular Lymphoid Tissue
Left Pubis Bone
Left Radius Bone
Left Retroperitoneal Lymphoid Tissue
Left Rib 1 Bone
Left Rib 10 Bone
Left Rib 11 Bone
Left Rib 12 Bone
Left Rib 2 Bone
Left Rib 3 Bone
Left Rib 4 Bone
Left Rib 5 Bone
Left Rib 6 Bone
Left Rib 7 Bone
Left Rib 8 Bone
Left Rib 9 Bone
Anterior Medial Left Scalp Skin
Anterior Midline Left Scalp Skin
Anterior Lateral Left Scalp Skin
Posterior Lateral Left Scalp Skin
Posterior Medial Left Scalp Skin
Posterior Midline Left Scalp Skin
Left Scaphoid Bone
Left Scapula Or Shoulder Blade Bone
Anterior Medial Left Shoulder Skin
Anterior Midline Left Shoulder Skin
Anterior Lateral Left Shoulder Skin
Posterior Lateral Left Shoulder Skin
Posterior Midline Left Shoulder Skin
Posterior Medial Left Shoulder Skin
Left Small Intestine
Left Sphenoid Bone
Left Spleen Lymphoid Tissue
Left Spleen
Left Splenic Hilar Lymphoid Tissue
Left Stapes Bone
Left Stomach
Left Submandibular Lymphoid Tissue
Left Submental Lymphoid Tissue
Left Supraclavicular Lymphoid Tissue
Left Talus Bone
Left Temporal Bone
Left Testis
Left Thymic Lymphoid Tissue
Left Tibia Bone
Left Tonsils Lymphoid Tissue
Left Trapezium Bone
Left Trapezoid Bone
Left Triquetral Bone
Left Ulna Bone
Anterior Medial Left Upper Arm Skin
Anterior Midline Left Upper Arm Skin
Anterior Lateral Left Upper Arm Skin
Posterior Lateral Left Upper Arm Skin
Posterior Midline Left Upper Arm Skin
Posterior Medial Left Upper Arm Skin
Anterior Medial Left Upper Leg (Anterior And Posterior Thigh) Skin
Anterior Midline Left Upper Leg (Anterior And Posterior Thigh) Skin
Anterior Lateral Left Upper Leg (Anterior And Posterior Thigh) Skin
Posterior Lateral Left Upper Leg (Anterior And Posterior Thigh) Skin
Posterior Midline Left Upper Leg (Anterior And Posterior Thigh) Skin
Posterior Medial Left Upper Leg (Anterior And Posterior Thigh) Skin
Left Vomer Bone
Left Waldeyer Ring Lymphoid Tissue
Anterior Medial Left Wrist Skin
Anterior Left Wrist Skin
Anterior Midline Left Wrist Skin
Anterior Lateral Left Wrist Skin
Posterior Lateral Left Wrist Skin
Posterior Midline Left Wrist Skin
Posterior Medial Left Wrist Skin
Left Zygomatic Bone
Anterior Midline Abdomen Skin
Midline Abdominal Lymphoid Tissue
Posterior Midline Back Skin
Midline Bladder
Posterior Midline Buttocks Skin
Midline Celiac Lymphoid Tissue
Anterior Midline Chest Skin
Anterior Midline Chin Skin
Midline Coccyx Bone
Midline Ethmoid Bone
Anterior Midline Forehead Skin
Midline Frontal Bone
Midline Gallbladder
Anterior Midline Genitalia Skin
Posterior Midline Genitalia Skin
Midline Heart
Midline Hilar Lymphoid Tissue
Midline Hyoid Bone
Midline Large Intestine
Anterior Midline Lip Skin
Midline Liver
Midline Mandible Bone
Midline Maxilla Bone
Midline Mesenteric Lymphoid Tissue
Anterior Midline Neck Skin
Posterior Midline Neck Skin
Anterior Midline Nose Skin
Midline Occipital Bone
Midline Ossa Coxae Bone
Midline Pancreas
Midline Paraaortic Lymphoid Tissue
Midline Porta Hepatis Lymphoid Tissue
Midline Retroperitoneal Lymphoid Tissue
Midline Sacrum Bone
Anterior Midline Scalp Skin
Posterior Midline Scalp Skin
Midline Small Intestine
Midline Sternum Bone
Midline Stomach
Anterior Lateral Right Abdomen Skin
Anterior Midline Right Abdomen Skin
Right Abdomen Skin
Anterior Medial Right Abdomen Skin
Right Abdominal Lymphoid Tissue
Right Adenoid Lymphoid Tissue
Right Adrenal
Anterior Lateral Right Ankle Skin
Anterior Midline Right Ankle Skin
Anterior Medial Right Ankle Skin
Posterior Medial Right Ankle Skin
Posterior Midline Right Ankle Skin
Posterior Lateral Right Ankle Skin
Right Axillary Lymphoid Tissue
Medial Right Back Skin
Midline Right Back Skin
Lateral Right Back Skin
Right Bladder
Right Brachial Lymphoid Tissue
Medial Right Buttocks Skin
Midline Right Buttocks Skin
Posterior Lateral Right Buttocks Skin
Right Calcaneus Bone
Right Capitate Bone
Right Celiac Lymphoid Tissue
Anterior Lateral Right Cheek Skin
Anterior Midline Right Cheek Skin
Anterior Medial Right Cheek Skin
Anterior Lateral Right Chest Skin
Anterior Midline Right Chest Skin
Anterior Medial Right Chest Skin
Anterior Lateral Right Chin Skin
Anterior Midline Right Chin Skin
Anterior Medial Right Chin Skin
Anterior Right Chin Skin
Right Clavicle Or Collarbone Bone
Right Cuboid Bone
Anterior Lateral Right Ear Skin
Anterior Midline Right Ear Skin
Anterior Medial Right Ear Skin
Posterior Medial Right Ear Skin
Posterior Lateral Right Ear Skin
Anterior Lateral Right Elbow Skin
Anterior Right Elbow Skin
Anterior Midline Right Elbow Skin
Anterior Medial Right Elbow Skin
Posterior Medial Right Elbow Skin
Posterior Midline Right Elbow Skin
Posterior Lateral Right Elbow Skin
Right Epitrochlear Lymphoid Tissue
Right Ethmoid Bone
Anterior Lateral Right Eyebrow Skin
Anterior Midline Right Eyebrow Skin
Anterior Medial Right Eyebrow Skin
Anterior Lateral Right Eyelid Skin
Anterior Midline Right Eyelid Skin
Anterior Medial Right Eyelid Skin
Right Femoral Lymphoid Tissue
Right Femur Bone
Right Fibula Bone
Anterior Lateral Right Foot And Toes Skin
Anterior Midline Right Foot And Toes Skin
Anterior Medial Right Foot And Toes Skin
Posterior Midline Right Foot And Toes Skin
Posterior Lateral Right Foot And Toes Skin
Right Foot Distal Phalange 1 Bone
Right Foot Distal Phalange 2 Bone
Right Foot Distal Phalange 3 Bone
Right Foot Distal Phalange 4 Bone
Right Foot Distal Phalange 5 Bone
Right Foot Middle Phalange 2 Bone
Right Foot Middle Phalange 3 Bone
Right Foot Middle Phalange 4 Bone
Right Foot Middle Phalange 5 Bone
Right Foot Proximal Phalange 1 Bone
Right Foot Proximal Phalange 2 Bone
Right Foot Proximal Phalange 3 Bone
Right Foot Proximal Phalange 4 Bone
Right Foot Proximal Phalange 5 Bone
Anterior Lateral Right Forearm Skin
Anterior Midline Right Forearm Skin
Anterior Medial Right Forearm Skin
Posterior Medial Right Forearm Skin
Posterior Midline Right Forearm Skin
Posterior Lateral Right Forearm Skin
Lateral Right Forehead Skin
Anterior Lateral Right Forehead Skin
Anterior Midline Right Forehead Skin
Anterior Medial Right Forehead Skin
Right Frontal Bone
Right Gallbladder
Anterior Lateral Right Genitalia Skin
Midline Right Genitalia Skin
Anterior Midline Right Genitalia Skin
Posterior Midline Right Genitalia Skin
Posterior Medial Right Genitalia Skin
Posterior Lateral Right Genitalia Skin
Right Hamate Bone
Anterior Lateral Right Hand And Fingers Skin
Anterior Midline Right Hand And Fingers Skin
Anterior Medial Right Hand And Fingers Skin
Posterior Medial Right Hand And Fingers Skin
Posterior Midline Right Hand And Fingers Skin
Posterior Lateral Right Hand And Fingers Skin
Right Hand Distal Phalange 1 Bone
Right Hand Distal Phalange 2 Bone
Right Hand Distal Phalange 3 Bone
Right Hand Distal Phalange 4 Bone
Right Hand Distal Phalange 5 Bone
Right Hand Middle Phalange 2 Bone
Right Hand Middle Phalange 3 Bone
Right Hand Middle Phalange 4 Bone
Right Hand Middle Phalange 5 Bone
Right Hand Proximal Phalange 1 Bone
Right Hand Proximal Phalange 2 Bone
Right Hand Proximal Phalange 3 Bone
Right Hand Proximal Phalange 4 Bone
Right Hand Proximal Phalange 5 Bone
Right Heart
Right Hilar Lymphoid Tissue
Right Humerus Bone
Right Iliac Lymphoid Tissue
Right Ilium Bone
Right Incus Bone
Right Inferior Nasal Conchae Bone
Right Infraclavicular Lymphoid Tissue
Right Inguinal Lymphoid Tissue
Right Intermediate Cuneiform Bone
Right Ischium Bone
Right Kidney
Anterior Lateral Right Knee Skin
Anterior Midline Right Knee Skin
Anterior Medial Right Knee Skin
Posterior Medial Right Knee Skin
Posterior Midline Right Knee Skin
Posterior Lateral Right Knee Skin
Right Lacrimal Bone
Right Large Intestine
Right Lateral Cuneiform Bone
Right Level Ii Cervical Lymphoid Tissue
Right Level Iii Cervical Lymphoid Tissue
Right Level Iv Cervical Lymphoid Tissue
Right Level V Cervical Lymphoid Tissue
Right Level Vi Cervical Lymphoid Tissue
Right Level Vii Cervical Lymphoid Tissue
Right Lingual Tonsils Lymphoid Tissue
Anterior Lateral Right Lip Skin
Anterior Midline Right Lip Skin
Anterior Medial Right Lip Skin
Right Liver
Anterior Lateral Right Lower Leg (Shin And Calf) Skin
Anterior Midline Right Lower Leg (Shin And Calf) Skin
Anterior Medial Right Lower Leg (Shin And Calf) Skin
Posterior Medial Right Lower Leg (Shin And Calf) Skin
Posterior Midline Right Lower Leg (Shin And Calf) Skin
Posterior Lateral Right Lower Leg (Shin And Calf) Skin
Right Lunate Bone
Right Lungs
Right Malleus Bone
Right Mandible Bone
Right Maxilla Bone
Right Medial Cuneiform Bone
Right Mesenteric Lymphoid Tissue
Right Metacarpal 1 Bone
Right Metacarpal 2 Bone
Right Metacarpal 3 Bone
Right Metacarpal 4 Bone
Right Metacarpal 5 Bone
Right Metatarsal 1 Bone
Right Metatarsal 2 Bone
Right Metatarsal 3 Bone
Right Metatarsal 4 Bone
Right Metatarsal 5 Bone
Right Nasal Bone
Right Nasopharynx Lymphoid Tissue
Right Navicular Bone
Anterior Lateral Right Neck Skin
Anterior Right Neck Skin
Anterior Midline Right Neck Skin
Anterior Medial Right Neck Skin
Posterior Medial Right Neck Skin
Posterior Midline Right Neck Skin
Posterior Lateral Right Neck Skin
Anterior Lateral Right Nose Skin
Anterior Medial Right Nose Skin
Anterior Midline Right Nose Skin
Right Occipital Lymphoid Tissue
Right Occipital Bone
Right Ossa Coxae Bone
Right Ovary
Right Palatine Bone
Right Pancreas
Right Paraaortic Lymphoid Tissue
Right Parietal Bone
Right Parotid Lymphoid Tissue
Right Patella Bone
Right Pectoral Lymphoid Tissue
Right Peritracheal Lymphoid Tissue
Right Pisiform Bone
Right Popliteal Lymphoid Tissue
Right Porta Hepatis Lymphoid Tissue
Right Preauricular Lymphoid Tissue
Right Pubis Bone
Right Radius Bone
Right Retroperitoneal Lymphoid Tissue
Right Rib 1 Bone
Right Rib 10 Bone
Right Rib 11 Bone
Right Rib 12 Bone
Right Rib 2 Bone
Right Rib 3 Bone
Right Rib 4 Bone
Right Rib 5 Bone
Right Rib 6 Bone
Right Rib 7 Bone
Right Rib 8 Bone
Right Rib 9 Bone
Anterior Lateral Right Scalp Skin
Anterior Midline Right Scalp Skin
Anterior Medial Right Scalp Skin
Posterior Medial Right Scalp Skin
Posterior Midline Right Scalp Skin
Posterior Lateral Right Scalp Skin
Right Scaphoid Bone
Right Scapula Or Shoulder Blade Bone
Anterior Lateral Right Shoulder Skin
Anterior Midline Right Shoulder Skin
Anterior Medial Right Shoulder Skin
Posterior Medial Right Shoulder Skin
Posterior Midline Right Shoulder Skin
Posterior Lateral Right Shoulder Skin
Right Small Intestine
Right Sphenoid Bone
Right Spleen Lymphoid Tissue
Right Spleen
Right Splenic Hilar Lymphoid Tissue
Right Stapes Bone
Right Stomach
Right Submandibular Lymphoid Tissue
Right Submental Lymphoid Tissue
Right Supraclavicular Lymphoid Tissue
Right Talus Bone
Right Temporal Bone
Right Testis
Right Thymic Lymphoid Tissue
Right Tibia Bone
Right Tonsils Lymphoid Tissue
Right Trapezium Bone
Right Trapezoid Bone
Right Triquetral Bone
Right Ulna Bone
Anterior Lateral Right Upper Arm Skin
Anterior Midline Right Upper Arm Skin
Anterior Medial Right Upper Arm Skin
Posterior Medial Right Upper Arm Skin
Posterior Midline Right Upper Arm Skin
Posterior Lateral Right Upper Arm Skin
Anterior Lateral Right Upper Leg (Anterior And Posterior Thigh) Skin
Anterior Midline Right Upper Leg (Anterior And Posterior Thigh) Skin
Anterior Medial Right Upper Leg (Anterior And Posterior Thigh) Skin
Posterior Medial Right Upper Leg (Anterior And Posterior Thigh) Skin
Posterior Midline Right Upper Leg (Anterior And Posterior Thigh) Skin
Posterior Lateral Right Upper Leg (Anterior And Posterior Thigh) Skin
Right Vomer Bone
Right Waldeyer Ring Lymphoid Tissue
Anterior Lateral Right Wrist Skin
Anterior Midline Right Wrist Skin
Anterior Medial Right Wrist Skin
Posterior Medial Right Wrist Skin
Posterior Midline Right Wrist Skin
Posterior Lateral Right Wrist Skin
Right Zygomatic Bone
Abdomen Skin
Abdominal Lymphoid Tissue
Adenoid Lymphoid Tissue
Anus
Back Skin
Bladder
Brain
Buttocks Skin
Celiac Lymphoid Tissue
Cerebrospinal Fluid
Cervical Vertebrae 1 Bone
Cervical Vertebrae 2 Bone
Cervical Vertebrae 3 Bone
Cervical Vertebrae 4 Bone
Cervical Vertebrae 5 Bone
Cervical Vertebrae 6 Bone
Cervical Vertebrae 7 Bone
Cervix
Chest Skin
Chin Skin
Esophagus
Forehead Skin
Gallbladder
Genitalia Skin
Heart
Hilar Lymphoid Tissue
Large Intestine
Leptomeningeal
Lingual Tonsils Lymphoid Tissue
Lip Skin
Liver
Lumbar Vertebrae 1 Bone
Lumbar Vertebrae 2 Bone
Lumbar Vertebrae 3 Bone
Lumbar Vertebrae 4 Bone
Lumbar Vertebrae 5 Bone
Mesenteric Lymphoid Tissue
Nasal Mucosa
Nasopharynx Lymphoid Tissue
Neck Skin
Posterior Neck Skin
Nose Skin
Oral Mucosa
Pancreas
Paraaortic Lymphoid Tissue
Porta Hepatis Lymphoid Tissue
Retroperitoneal Lymphoid Tissue
Scalp Skin
Posterior Scalp Skin
Small Intestine
Spinal Cord
Spleen Lymphoid Tissue
Stomach
Thoracic Vertebrae 1 Bone
Thoracic Vertebrae 10 Bone
Thoracic Vertebrae 11 Bone
Thoracic Vertebrae 12 Bone
Thoracic Vertebrae 2 Bone
Thoracic Vertebrae 3 Bone
Thoracic Vertebrae 4 Bone
Thoracic Vertebrae 5 Bone
Thoracic Vertebrae 6 Bone
Thoracic Vertebrae 7 Bone
Thoracic Vertebrae 8 Bone
Thoracic Vertebrae 9 Bone
Tonsils Lymphoid Tissue
Vagina
Waldeyer Ring Lymphoid Tissue
Table 2: Anatomical Structures. Listed are the 651 distinct anatomical structures displayed in the BodyMapR package.
To construct a data visualization of these anatomical structures, individual structures were mapped to the Body Map using an X-Y grid-based coordinate system. To assist in topographical mapping, an interactive coordinate system was generated via plotly15 (Figure 4).
Figure 4: Code for the interactive plotly X-Y coordinate system for the Body Map topographical image
body_map.png <-  BodyMapR::BodyMapR_biorender.png

grid.2 <- data.frame(x = rep((seq(from = 1, to = 100, by = 1)), 
                             each = 100),
                     y = rep((seq(from = 1, to = 100, by = 1)), 
                             len = 100))

df.grid <- data.frame()

grid.plotly <- ggplot(df.grid) + 
  xlim(0, 100) + 
  ylim(0, 100) +
  theme_bw() +
  theme(panel.border = element_blank(), 
        panel.grid.major = element_blank(), 
        panel.grid.minor = element_blank(), 
        axis.line = element_blank()) +
  theme(axis.text.x = element_blank(),
        axis.text.y = element_blank(),
        axis.ticks = element_blank(),
        axis.title = element_blank()) +
  annotation_raster(body_map.png,
                    ymin = 0,
                    xmin = 0,
                    xmax = 100,
                    ymax = 100) +
  geom_point(data = grid.2,
             aes(x = x,
                 y = y))

ggplotly(grid.plotly)
As seen in Figure 5, individual X-Y coordinates are visualized by utilizing the hover text functionality of plotly.
Figure 5: Interactive plotly X-Y coordinate system for the Body Map topographical image.
Coordinate-System-for-BioRender-BodyMap-HTML-for-Figure-width-9.knit