R/network_utils.R

In DivadNojnarg/CaPO4Sim: A Virtual Patient Simulator in the Context of Calcium and Phosphate Homeostasis

#' @title CaPO4 Network Generator
#'
#' @description Create a CaPO4 network taking nodes and edges as inputs
#'
#' @param nodes A dataframe of nodes provided by \link{generate_nodes}.
#' @param edges A dataframe of edges provided by \link{generate_edges}.
#' @param usephysics Whether to use physic. FALSE by default. A visNetwork API parameter.
#' @param isMobile Shiny input checking if the app is running on a cellphone/tablet.
#'
#' @export
generate_network <- function(nodes, edges, usephysics = FALSE, isMobile) {
  visNetwork::visNetwork(
    nodes,
    edges,
    width = "100%",
    height = "100vh"
  ) %>%
    visNetwork::visNodes(
      shapeProperties = list(
        useBorderWithImage = FALSE,
        interpolation = FALSE
      )
    ) %>%
    # put shadow on false
    visNetwork::visEdges(
      shadow = FALSE,
      font = list(align = "horizontal")
    ) %>%
    # add group selection option
    visNetwork::visOptions(
      highlightNearest = FALSE,
      clickToUse = FALSE,
      manipulation = FALSE,
      collapse = FALSE,
      autoResize = if (isMobile()) FALSE else TRUE
    ) %>%
    # prevent edge from being selected when a node is selected
    visNetwork::visInteraction(
      hover = TRUE,
      hoverConnectedEdges = FALSE,
      selectConnectedEdges = FALSE,
      multiselect = FALSE,
      dragNodes = FALSE,
      dragView = FALSE,
      zoomView = FALSE,
      navigationButtons = FALSE,
      selectable = TRUE,
      tooltipStyle = '
        position: fixed;
        top: 50px;
        left: 50%;
        width: 50%;
        transform: translate(-50%, -50%);
        visibility: hidden;
        padding: 5px;
        padding-right: 10px;
        padding-bottom: 10px;
        white-space: nowrap;
        font-family: verdana;
        font-size: 14px;
        font-color: #000000;
        background-color: #FFFFFF;
        -moz-border-radius: 3px;
        -webkit-border-radius: 3px;
        border-radius: 3px;
        border: 1px solid #808074;
        box-shadow: 3px 3px 10px rgba(0, 0, 0, 0.2);
        z-index: 100;'
    ) %>%
    # stabilization prevents arrows from bouncing
    visNetwork::visPhysics(stabilization = TRUE, enabled = usephysics)
}

#' @title CaPO4 Nodes Generator
#'
#' @description Generate nodes for the CaPO4 network
#'
#' @param components Shiny input CaPO4 component selector. See \link{networkOptions}.
#' @param organs Shiny input to toggle organs display. See \link{networkOptions}.
#' @param regulations Shiny input to toggle hormone display. See \link{networkOptions}.
#' @param background Shiny input background selector. See \link{networkOptions}.
#' @param diseases Shiny input disease selector. See \link{diseaseSelect}.
#' @param organs_nodes_size Shiny input for organs node size. See \link{networkOptions}.
#' @param hormones_nodes_size Shiny input for hormones node size. See \link{networkOptions}..
#'
#' @export
generate_nodes <- function(
  components,
  organs,
  regulations,
  background,
  diseases,
  organs_nodes_size,
  hormones_nodes_size
) {
  req(organs_nodes_size(), hormones_nodes_size())

  data.frame(
    id = 1:16,
    shape = c(
      "image",
      "image",
      "image",
      "image",
      "image",
      "image",
      "image",
      "image",
      ifelse(regulations(), "image", "text"),
      ifelse(regulations(), "image", "text"),
      "image",
      ifelse(regulations(), "image", "text"),
      ifelse(regulations(), "image", "text"),
      ifelse(regulations(), "image", "text"),
      ifelse(regulations(), "image", "text"),
      ifelse(regulations(), "image", "text")
    ),
    image = c(
      "CaPO4_network/intestine.svg",
      "CaPO4_network/plasma.svg",
      "CaPO4_network/rapid-bone.svg",
      "CaPO4_network/bone.svg",
      "CaPO4_network/kidney.svg",
      "CaPO4_network/kidney_zoom1.svg",
      "CaPO4_network/urine.svg",
      "CaPO4_network/cells.svg",
      "CaPO4_network/Cap.svg",
      "CaPO4_network/PO4.svg",
      if (is.null(background())) {
        "CaPO4_network/parathyroid_gland.svg"
      } else if (background() == "rat") {
        "CaPO4_network/parathyroid_gland.svg"
      } else {
        "CaPO4_network/parathyroid_gland_human.svg"
      },
      "CaPO4_network/PTH.svg",
      "CaPO4_network/D3.svg",
      "CaPO4_network/D3.svg",
      "CaPO4_network/D3.svg",
      "CaPO4_network/FGF23.svg"
    ),
    label = c(rep("", 6), rep("", 10)),
    fixed = list("x" = TRUE, "y" = TRUE),
    # node position tighlty depends on the selected background
    x = if (is.null(background())) {
      c(
        38,
        -65,
        -65,
        -256,
        180,
        360,
        170,
        -190,
        290,
        320,
        41,
        -418,
        330,
        385,
        -386,
        481
      )
    } else if (background() == "rat") {
      c(
        38,
        -65,
        -65,
        -256,
        180,
        360,
        170,
        -190,
        290,
        320,
        41,
        -418,
        330,
        385,
        -386,
        481
      )
    } else {
      c(
        13,
        -80,
        -185,
        -322,
        157,
        333,
        7,
        -175,
        290,
        320,
        9,
        -466,
        330,
        385,
        -386,
        481
      )
    },

    y = if (is.null(background())) {
      c(
        -150,
        195,
        472,
        460,
        0,
        230,
        506,
        0,
        -317,
        -633,
        -452,
        240,
        -452,
        0,
        -106,
        -452
      )
    } else if (background() == "rat") {
      c(
        -150,
        195,
        472,
        460,
        0,
        230,
        506,
        0,
        -317,
        -633,
        -452,
        240,
        -452,
        0,
        -106,
        -452
      )
    } else {
      c(
        23,
        320,
        524,
        214,
        189,
        439,
        581,
        88,
        -317,
        -633,
        -449,
        400,
        -452,
        0,
        -106,
        -452
      )
    },

    color = list(
      background = "#97C2FC",
      border = "#97C2FC",
      highlight = list(background = "orange", border = "orange")
    ),
    size = c(
      rep(organs_nodes_size(), 5),
      150,
      rep(organs_nodes_size(), 2),
      rep(hormones_nodes_size(), 2),
      organs_nodes_size(),
      rep(hormones_nodes_size(), 5)
    ),
    #fixed = list("x" = TRUE, "y" = TRUE),
    physics = rep(FALSE, 16),
    hidden = c(
      ## organs ##
      if (organs()) {
        c(
          rep(FALSE, 7),
          # PO4 Cells
          ifelse(
            is.element("PO4", components()),
            ifelse(is.element("Ca", components()), FALSE, FALSE),
            TRUE
          )
        )
      } else {
        rep(TRUE, 8)
      },
      ## Hormones ##
      # Ca plasma
      ifelse(
        regulations(),
        ifelse(is.element("Ca", components()), FALSE, TRUE),
        TRUE
      ),
      # PO4 plasma
      ifelse(
        regulations(),
        ifelse(
          is.element("PO4", components()) &
            (
              is.element("D3", components()) |
                is.element("PTH", components()) |
                is.element("FGF23", components())
            ),
          FALSE,
          TRUE
        ),
        TRUE
      ),
      # PTHg
      ifelse(
        regulations(),
        ifelse(is.element("PTH", components()), FALSE, TRUE),
        TRUE
      ),
      # PTH plasma
      TRUE,
      # ifelse(organs(),
      #        ifelse(regulations(),
      #               ifelse(is.element("PTH", components()), FALSE, TRUE), TRUE), TRUE),
      # D3 regulation
      ifelse(
        regulations(),
        ifelse(
          is.element("D3", components()) &
            (
              is.element("PO4", components()) |
                is.element("Ca", components()) |
                is.element("PTH", components()) |
                is.element("FGF23", components())
            ),
          FALSE,
          TRUE
        ),
        TRUE
      ),
      # D3 plasma
      ifelse(
        organs(),
        ifelse(
          regulations(),
          ifelse(is.element("D3", components()), FALSE, TRUE),
          TRUE
        ),
        TRUE
      ),
      # D3 plasma
      ifelse(
        organs(),
        ifelse(
          regulations(),
          ifelse(is.element("D3", components()), FALSE, TRUE),
          TRUE
        ),
        TRUE
      ),
      # FGF23
      ifelse(
        regulations(),
        ifelse(is.element("FGF23", components()), FALSE, TRUE),
        TRUE
      )
    ),
    stringsAsFactors = FALSE
  )
}

#' @title CaPO4 Edges Generator
#'
#' @description Generate edges for the CaPO4 network
#'
#' @param components Shiny input CaPO4 component selector. See \link{networkOptions}.
#' @param organs Shiny input to toggle organs display. See \link{networkOptions}.
#' @param regulations Shiny input to toggle hormone display. See \link{networkOptions}.
#' @param diseases Shiny input disease selector. See \link{diseaseSelect}.
#' @param organs_edges_size Shiny input for organs edges size. See \link{networkOptions}.
#' @param hormones_edges_size Shiny input for hormones edges size. See \link{networkOptions}.
#'
#' @export
generate_edges <- function(
  components,
  organs,
  regulations,
  diseases,
  organs_edges_size,
  hormones_edges_size
) {
  req(organs_edges_size(), hormones_edges_size())
  data.frame(
    from = c(
      1,
      # change the from direction depending on the net flux result
      if (diseases$php1()) {
        2
      } else if (diseases$hypopara()) {
        3
      } else if (diseases$hypoD3()) {
        3
      } else {
        2
      },
      if (diseases$php1()) {
        2
      } else if (diseases$hypopara()) {
        3
      } else if (diseases$hypoD3()) {
        3
      } else {
        2
      },
      rep(3, 2),
      4,
      2,
      rep(5, 2),
      rep(5, 2),
      if (diseases$php1()) {
        2
      } else if (diseases$hypopara()) {
        8
      } else if (diseases$hypoD3()) {
        8
      } else {
        2
      },
      rep(9, 3),
      rep(10, 3),
      rep(11, 2),
      11,
      rep(13, 2),
      rep(14, 2),
      rep(15, 2),
      rep(16, 2)
    ),

    to = c(
      2,
      if (diseases$php1()) {
        3
      } else if (diseases$hypopara()) {
        2
      } else if (diseases$hypoD3()) {
        2
      } else {
        3
      },
      if (diseases$php1()) {
        3
      } else if (diseases$hypopara()) {
        2
      } else if (diseases$hypoD3()) {
        2
      } else {
        3
      },
      rep(4, 2),
      2,
      5,
      rep(2, 2),
      rep(7, 2),
      if (diseases$php1()) {
        8
      } else if (diseases$hypopara()) {
        2
      } else if (diseases$hypoD3()) {
        2
      } else {
        8
      },
      11,
      5,
      13,
      11,
      13,
      16,
      5,
      13,
      4,
      11,
      16,
      14,
      5,
      4,
      1,
      13,
      5
    ),

    arrows = list(
      to = list(
        enabled = c(
          TRUE,
          # show or hode arrow symbol depending on the net flux result
          rep(
            if (diseases$php1() | diseases$hypopara() | diseases$hypoD3())
              TRUE else FALSE,
            2
          ),
          rep(TRUE, 8),
          if (diseases$php1() | diseases$hypopara() | diseases$hypoD3())
            TRUE else FALSE,
          rep(TRUE, 17)
        ),
        scaleFactor = 1,
        type = "arrow"
      )
    ),

    label = c(
      "",
      "Net Ca",
      "Net PO4",
      "Ca",
      "PO4",
      rep("", 2),
      "Ca",
      "PO4",
      "Ca",
      "PO4",
      "Net PO4",
      rep("-", 3),
      "+",
      "-",
      "+",
      "",
      "+",
      "+",
      "-",
      "+",
      "-",
      "+",
      "+",
      "+",
      "-",
      "-"
    ),
    id = c(
      "Abs_int",
      "Net_Ca_pf",
      "Net_PO4_pf",
      "Ac_Ca",
      "Ac_PO4",
      "Res",
      7,
      "Reabs_Ca",
      "Reabs_PO4",
      "U_Ca",
      "U_PO4",
      "Net_PO4_cells",
      13:29
    ),
    width = c(rep(organs_edges_size(), 12), rep(hormones_edges_size(), 17)),
    font.size = c(rep(25, 12), rep(60, 17)),
    font.align = c(
      "",
      if (!diseases$hypopara() | !diseases$hypoD3()) "bottom" else "top",
      if (!diseases$hypopara() | !diseases$hypoD3()) "bottom" else "top",
      "top",
      "bottom",
      rep("", 4),
      "bottom",
      "top",
      "bottom",
      "bottom",
      rep("top", 2),
      "top",
      "top",
      "top",
      "",
      "bottom",
      "top",
      "top",
      "bottom",
      "bottom",
      "top",
      "top",
      rep("top", 2),
      "bottom"
    ),
    color = list(color = c(rep("black", 29)), highlight = "yellow"),
    dashes = c(rep(FALSE, 12), rep(TRUE, 17)),
    title = c(
      rep(NA, 3),
      rep(NA, 9),
      rep(NA, 2),
      rep(NA, 15)
    ),
    smooth = c(rep(TRUE, 29)),
    length = c(
      200,
      rep(300, 2),
      rep(300, 2),
      200,
      300,
      200,
      rep(300, 4),
      rep(200, 8),
      1800,
      rep(200, 8)
    ),
    # to show either Ca or PO4 or CaPO4 network arrows
    hidden = c(
      ## organ arrows ##
      if (organs()) {
        c(
          ifelse(
            is.element("Ca", components()) | is.element("PO4", components()),
            FALSE,
            TRUE
          ),
          ifelse(
            is.element("Ca", components()),
            ifelse(is.element("PO4", components()), FALSE, FALSE),
            TRUE
          ),
          ifelse(
            is.element("PO4", components()),
            ifelse(is.element("Ca", components()), FALSE, FALSE),
            TRUE
          ),
          ifelse(
            is.element("Ca", components()),
            ifelse(is.element("PO4", components()), FALSE, FALSE),
            TRUE
          ),
          ifelse(
            is.element("PO4", components()),
            ifelse(is.element("Ca", components()), FALSE, FALSE),
            TRUE
          ),
          rep(
            ifelse(
              is.element("Ca", components()) | is.element("PO4", components()),
              FALSE,
              TRUE
            ),
            2
          ),
          ifelse(
            is.element("Ca", components()),
            ifelse(is.element("PO4", components()), FALSE, FALSE),
            TRUE
          ),
          ifelse(
            is.element("PO4", components()),
            ifelse(is.element("Ca", components()), FALSE, FALSE),
            TRUE
          ),
          ifelse(
            is.element("Ca", components()),
            ifelse(is.element("PO4", components()), FALSE, FALSE),
            TRUE
          ),
          rep(
            ifelse(
              is.element("PO4", components()),
              ifelse(is.element("Ca", components()), FALSE, FALSE),
              TRUE
            ),
            2
          )
        )
      } else {
        rep(TRUE, 12)
      },

      ## hormonal regulations arrows ##
      # Ca regulation to PTH
      ifelse(
        regulations(),
        ifelse(
          is.element("PTH", components()) & is.element("Ca", components()),
          FALSE,
          TRUE
        ),
        TRUE
      ),
      # Ca to Kidney
      ifelse(
        organs(),
        ifelse(
          regulations(),
          ifelse(is.element("Ca", components()), FALSE, TRUE),
          TRUE
        ),
        TRUE
      ),
      # Ca regulation to D3
      ifelse(
        regulations(),
        ifelse(
          is.element("D3", components()) & is.element("Ca", components()),
          FALSE,
          TRUE
        ),
        TRUE
      ),
      # PO4 regulation to PTH
      ifelse(
        regulations(),
        ifelse(
          is.element("PTH", components()) & is.element("PO4", components()),
          FALSE,
          TRUE
        ),
        TRUE
      ),
      # PO4 regulation to D3
      ifelse(
        regulations(),
        ifelse(
          is.element("D3", components()) & is.element("PO4", components()),
          FALSE,
          TRUE
        ),
        TRUE
      ),
      # PO4 regulation to FGF23
      ifelse(
        regulations(),
        ifelse(
          is.element("FGF23", components()) & is.element("PO4", components()),
          FALSE,
          TRUE
        ),
        TRUE
      ),
      # PTH regulation to kidney
      ifelse(
        organs(),
        ifelse(
          regulations(),
          ifelse(is.element("PTH", components()), FALSE, TRUE),
          TRUE
        ),
        TRUE
      ),
      # PTH regulation to D3
      ifelse(
        regulations(),
        ifelse(
          is.element("D3", components()) & is.element("PTH", components()),
          FALSE,
          TRUE
        ),
        TRUE
      ),
      # PTH regulation to bone
      ifelse(
        organs(),
        ifelse(
          regulations(),
          ifelse(is.element("PTH", components()), FALSE, TRUE),
          TRUE
        ),
        TRUE
      ),
      # D3 regulation to PTH
      ifelse(
        regulations(),
        ifelse(
          is.element("PTH", components()) & is.element("D3", components()),
          FALSE,
          TRUE
        ),
        TRUE
      ),
      # D3 regulation to FGF23
      ifelse(
        regulations(),
        ifelse(
          is.element("FGF23", components()) & is.element("D3", components()),
          FALSE,
          TRUE
        ),
        TRUE
      ),
      # D3 regulation to D3
      ifelse(
        organs(),
        ifelse(
          regulations(),
          ifelse(is.element("D3", components()), FALSE, TRUE),
          TRUE
        ),
        TRUE
      ),
      # D3 regulation to kidney
      ifelse(
        organs(),
        ifelse(
          regulations(),
          ifelse(is.element("D3", components()), FALSE, TRUE),
          TRUE
        ),
        TRUE
      ),
      # D3 regulation to bone
      ifelse(
        organs(),
        ifelse(
          regulations(),
          ifelse(is.element("D3", components()), FALSE, TRUE),
          TRUE
        ),
        TRUE
      ),
      # D3 regulation to intestine
      ifelse(
        organs(),
        ifelse(
          regulations(),
          ifelse(is.element("D3", components()), FALSE, TRUE),
          TRUE
        ),
        TRUE
      ),
      # FGF regulation to D3
      ifelse(
        regulations(),
        ifelse(
          is.element("D3", components()) & is.element("FGF23", components()),
          FALSE,
          TRUE
        ),
        TRUE
      ),
      # FGF regulation to kidney
      ifelse(
        organs(),
        ifelse(
          regulations(),
          ifelse(is.element("FGF23", components()), FALSE, TRUE),
          TRUE
        ),
        TRUE
      )
    ),
    stringsAsFactors = FALSE
  )
}