## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)

## ----protein_design_explorer--------------------------------------------------
# library(rMosaic)
# 
# protein_data_url <- "https://idl.uw.edu/mosaic/data/protein-design.parquet"
# 
# protein_spec <- list(
#   meta = list(
#     title = "Protein Design Explorer",
#     description = paste(
#       "Explore synthesized proteins generated via RFDiffusion.",
#       "Minibinders are small proteins that bind to a specific protein target.",
#       "The dashboard links parameter menus, marginal histograms, a pLDDT vs. pAE raster plot, and a table of selected designs.",
#       sep = "\n\n"
#     ),
#     credit = paste(
#       "Adapted from a UW CSE 512 project by Christina Savvides,",
#       "Alexander Shida, Riti Biswas, and Nora McNamara-Bordewick.",
#       "Data from the UW Institute for Protein Design."
#     )
#   ),
#   data = list(
#     proteins = list(file = protein_data_url)
#   ),
#   params = list(
#     query = list(select = "crossfilter"),
#     point = list(select = "intersect", empty = TRUE),
#     plddt_domain = c(67, 94.5),
#     pae_domain = c(5, 29),
#     scheme = "observable10"
#   ),
#   vconcat = list(
#     # Parameter menus filter all downstream views.
#     list(
#       hconcat = list(
#         list(
#           input = "menu",
#           from = "proteins",
#           column = "partial_t",
#           label = "Partial t",
#           as = "$query"
#         ),
#         list(
#           input = "menu",
#           from = "proteins",
#           column = "noise",
#           label = "Noise",
#           as = "$query"
#         ),
#         list(
#           input = "menu",
#           from = "proteins",
#           column = "gradient_decay_function",
#           label = "Gradient Decay",
#           as = "$query"
#         ),
#         list(
#           input = "menu",
#           from = "proteins",
#           column = "gradient_scale",
#           label = "Gradient Scale",
#           as = "$query"
#         )
#       )
#     ),
#     list(vspace = "1.5em"),
#     # Top marginal histogram for pLDDT.
#     list(
#       hconcat = list(
#         list(
#           plot = list(
#             list(
#               mark = "rectY",
#               data = list(from = "proteins", filterBy = "$query"),
#               x = list(bin = "plddt_total", steps = 60),
#               y = list(count = NULL),
#               z = "version",
#               fill = "version",
#               order = "z",
#               reverse = TRUE,
#               insetLeft = 0.5,
#               insetRight = 0.5
#             )
#           ),
#           width = 600,
#           height = 55,
#           xAxis = NULL,
#           yAxis = NULL,
#           xDomain = "$plddt_domain",
#           colorDomain = "Fixed",
#           colorScheme = "$scheme",
#           marginLeft = 40,
#           marginRight = 0,
#           marginTop = 0,
#           marginBottom = 0
#         ),
#         list(hspace = 5),
#         list(
#           legend = "color",
#           `for` = "scatter",
#           columns = 1,
#           as = "$query"
#         )
#       )
#     ),
#     # Main raster scatterplot plus right marginal histogram for pAE.
#     list(
#       hconcat = list(
#         list(
#           name = "scatter",
#           plot = list(
#             list(mark = "frame", stroke = "#ccc"),
#             list(
#               mark = "raster",
#               data = list(from = "proteins", filterBy = "$query"),
#               x = "plddt_total",
#               y = "pae_interaction",
#               fill = "version",
#               pad = 0
#             ),
#             list(
#               select = "intervalXY",
#               as = "$query",
#               brush = list(stroke = "currentColor", fill = "transparent")
#             ),
#             list(
#               mark = "dot",
#               data = list(from = "proteins", filterBy = "$point"),
#               x = "plddt_total",
#               y = "pae_interaction",
#               fill = "version",
#               stroke = "currentColor",
#               strokeWidth = 0.5
#             )
#           ),
#           opacityDomain = c(0, 2),
#           opacityClamp = TRUE,
#           colorDomain = "Fixed",
#           colorScheme = "$scheme",
#           xDomain = "$plddt_domain",
#           yDomain = "$pae_domain",
#           xLabelAnchor = "center",
#           yLabelAnchor = "center",
#           marginTop = 0,
#           marginLeft = 40,
#           marginRight = 0,
#           width = 600,
#           height = 450
#         ),
#         list(
#           plot = list(
#             list(
#               mark = "rectX",
#               data = list(from = "proteins", filterBy = "$query"),
#               x = list(count = NULL),
#               y = list(bin = "pae_interaction", steps = 60),
#               z = "version",
#               fill = "version",
#               order = "z",
#               reverse = TRUE,
#               insetTop = 0.5,
#               insetBottom = 0.5
#             )
#           ),
#           width = 55,
#           height = 450,
#           xAxis = NULL,
#           yAxis = NULL,
#           marginTop = 0,
#           marginLeft = 0,
#           marginRight = 0,
#           yDomain = "$pae_domain",
#           colorDomain = "Fixed",
#           colorScheme = "$scheme"
#         )
#       )
#     ),
#     list(vspace = "1em"),
#     list(
#       input = "table",
#       as = "$point",
#       filterBy = "$query",
#       from = "proteins",
#       columns = c(
#         "version",
#         "pae_interaction",
#         "plddt_total",
#         "noise",
#         "gradient_decay_function",
#         "gradient_scale",
#         "movement"
#       ),
#       width = 680,
#       height = 215
#     )
#   )
# )
# 
# runMosaicApp(
#   spec = protein_spec,
#   specType = "yaml",
#   data = NULL,
#   title = "Protein Design Explorer",
#   backend = "wasm",
#   height = "900px"
# )