R/nPOD_DIVE.R

In avucoh/nPOD: What the Package Does (One Line, Title Case)

# shared configs
shared_config <- function() list(data = cdata,
                                 factorx = "type$|grp$|cat$|score$|grade$|bin$|pos$|^male$|^sex$|^race$|risk$",
                                 colors = c("Autoab Pos" = "orange",
                                            "Cystic fibrosis" = "aquamarine4",
                                            "Gastric Bypass" = "bisque4",
                                            "Gestational diabetes" = "deeppink2",
                                            "Monogenic Diabetes" = "red4",
                                            "No diabetes" = "royalblue2",
                                            "Other-Diabetes" = "indianred4",
                                            "Other-No Diabetes" = "steelblue2",
                                            "T1D" = "red",
                                            "T1D Medalist" = "maroon",
                                            "T2D" = "purple",
                                            "Pending" = "gray",
                                            "Pregnancy" = "pink",
                                            "Transplant" = "darkseagreen4"))

#' Run app locally
#' @export
nPOD_DataView <- function() suppressWarnings(runApp(appDir = system.file("app", package = "nPOD")))

#' matrixMix config
#' @export
matrixMix_config <- function() list(M = cordata$M,
                                    N = cordata$N,
                                    cdata = shared_config()$data,
                                    metadata = matrix_metadata,
                                    vkey = "VarID",
                                    # widgetopt = "CellTissue",
                                    # widgetdata = system.file("www/", "test.json", package = "DIVE"),
                                    factorx = shared_config()$factorx,
                                    dcolors = list(donor.type = shared_config()$colors))


#' Launch DIVE matrix module with nPOD data
#'
#' @export
matrixMixR <- function() do.call(DIVE::matrixMixR, c(ns = "nPOD", matrixMix_config()))

##-----------------------------------------------------------------------------------------------------------------------------------------------------#

#' multiVUI app config
multiV_config <- function() list(hdata = hdata,
                                 hcat = list(Transcriptomics = list("Kodama et al. (2016)", "Holm et al. (2018)"),
                                             Proteomics = list("Liu et al. (2016)", "Nyalwidhe et al. (2017)")),
                                 cdata = shared_config()$data,
                                 factorx = shared_config()$factorx,
                                 preselect = "donor.type")

#' Launch DIVE multi-view module with nPOD data
#'
#' @export
multiVUIR <- function() do.call(DIVE::multiVUIR, c(ns = "nPOD", multiV_config()))

##-----------------------------------------------------------------------------------------------------------------------------------------------------#

#' browseR config
#' @export
browse_config <- function() list(dt_id = cdata,
                                  index1 = "ID",
                                  index2 = "donor.type",
                                  dt_var = metadata_map,
                                  dt_var_index = "VarID",
                                  dt_var_ext = metadata_ext)

#' Launch DIVE browser module with nPOD data
#'
#' @export
browseR <- function() do.call(DIVE::browseR, c(ns = "nPOD", browse_config()))

##-----------------------------------------------------------------------------------------------------------------------------------------------------#

#' matchApp config
#' @export
matchApp_config <- function() list(subsets = list("No diabetes" = list("No diabetes", "Other-No Diabetes"),
                                                  "Autoantibody positive" = list("Autoab Pos"),
                                                  "Type 1 Diabetes" = list("T1D", "T1D Medalist", "Monogenic Diabetes"),
                                                  "Other diabetes" = list("T2D", "Gestational diabetes"),
                                                  "Other" = list("Transplant", "Cystic fibrosis", "Pregnancy", "Gastric Bypass")),
                                   refdata = npodX,
                                   datakey = "Cohort",
                                   xname = "CohortX",
                                   refname = "nPOD",
                                   HPCG = hpcg,
                                   colors = shared_config()$colors,
                                   vars = list(Clinical = c("BMI", "db.duration", "age.onset",
                                                            "Cpeptide", "HbA1c", "peak.gluc",
                                                            "GADA.pos", "IA2A.pos", "mIAA.pos", "ZnT8A.pos", "AutoAb.count"),
                                               Demographic = c("age", "sex_Female", "sex_Male",
                                                               "race_Caucasian", "race_AfricanAmerican", "race_Hispanic.Latino",
                                                               "race_Asian", "race_AmericanIndian", "race_Multiracial")),
                                   subsetfeat = "donor.type",
                                   factorx = shared_config()$factorx,
                                   appdata = "appdata/divid_coded.csv")

#' Launch DIVE match module with nPOD data
#'
#' @export
matchAppR <- function() do.call(DIVE::matchAppR, c(ns = "nPOD", matchApp_config()))