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Visualizing new version of IDEAFilter #247

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6df7069
Grab IDEAFilter for Github
Jeff-Thompson12 Aug 16, 2023
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Capture recent changes
Jeff-Thompson12 Aug 16, 2023
8bf38e0
Update IDEAFilter
Jeff-Thompson12 Sep 22, 2023
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2 changes: 2 additions & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,8 @@ import(R6)
import(dplyr)
import(shiny)
importFrom(GGally,ggsurv)
importFrom(IDEAFilter,IDEAFilter)
importFrom(IDEAFilter,IDEAFilter_ui)
importFrom(IDEAFilter,shiny_data_filter)
importFrom(IDEAFilter,shiny_data_filter_ui)
importFrom(cicerone,Cicerone)
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8 changes: 4 additions & 4 deletions R/mod_indvExp_srv.R
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Expand Up @@ -11,7 +11,7 @@

#' @import shiny
#' @import dplyr
#' @importFrom IDEAFilter shiny_data_filter
#' @importFrom IDEAFilter shiny_data_filter IDEAFilter

@AARON-CLARK AARON-CLARK Aug 21, 2023

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is shiny_data_filter still required?

Suggested change
#' @importFrom IDEAFilter shiny_data_filter IDEAFilter
#' @importFrom IDEAFilter IDEAFilter

#' @importFrom stringr str_detect
#' @importFrom purrr map update_list reduce
#' @importFrom shinyjs show hide
Expand Down Expand Up @@ -115,16 +115,16 @@ mod_indvExp_server <- function(input, output, session, datafile){


# Feed IDEAFilter! Returns data frame to use down stream... May be filtered or not
filtered_data <- callModule(
IDEAFilter::shiny_data_filter, # Module name
filtered_data <- IDEAFilter::IDEAFilter(
# IDEAFilter::shiny_data_filter, # Module name
"data_filter", # whatever you named the widget
data = feed_filter, # the name of your pre-processed data
verbose = FALSE)



observe({
req(!is.null(filtered_data())) # make sure we have an output data frame from IDEAFilter
req(filtered_data()) # make sure we have an output data frame from IDEAFilter

subj <- unique(filtered_data()$USUBJID) # get list of unique USUBJIDs

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4 changes: 2 additions & 2 deletions R/mod_indvExp_ui.R
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Expand Up @@ -11,7 +11,7 @@
#'
#' @import shiny
#' @importFrom shinyjs useShinyjs hidden
#' @importFrom IDEAFilter shiny_data_filter_ui
#' @importFrom IDEAFilter shiny_data_filter_ui IDEAFilter_ui

@AARON-CLARK AARON-CLARK Aug 21, 2023

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Is shiny_data_filter_ui still required?

Suggested change
#' @importFrom IDEAFilter shiny_data_filter_ui IDEAFilter_ui
#' @importFrom IDEAFilter IDEAFilter_ui

#' @importFrom shinyWidgets materialSwitch
#' @importFrom timevis timevisOutput
#' @importFrom plotly plotlyOutput
Expand Down Expand Up @@ -46,7 +46,7 @@ mod_indvExp_ui <- function(id){
),
conditionalPanel(condition = "input.filter_df != null", ns = ns,
div(id = "indv_cic_data_filter",
IDEAFilter::shiny_data_filter_ui(ns("data_filter"))
IDEAFilter::IDEAFilter_ui(ns("data_filter"))
)
)
),
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6 changes: 3 additions & 3 deletions R/mod_popExp.R
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Expand Up @@ -7,7 +7,7 @@
#'
#' @import shiny
#' @import dplyr
#' @importFrom IDEAFilter shiny_data_filter
#' @importFrom IDEAFilter shiny_data_filter IDEAFilter

@AARON-CLARK AARON-CLARK Aug 21, 2023

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is shiny_data_filter still required?

Suggested change
#' @importFrom IDEAFilter shiny_data_filter IDEAFilter
#' @importFrom IDEAFilter IDEAFilter

#' @importFrom haven zap_label zap_formats
#' @importFrom purrr map walk2
#' @importFrom plotly renderPlotly ggplotly layout
Expand Down Expand Up @@ -186,8 +186,8 @@ mod_popExp_server <- function(input, output, session, datafile) {
})

# Call IDEAFilter Module
filters <- callModule(
IDEAFilter::shiny_data_filter,
filters <- IDEAFilter::IDEAFilter(
# IDEAFilter::shiny_data_filter,
"data_filter", # whatever you named the widget
data = reactive(feed_filter()[filter_cols()]), # the name of your pre-processed data
verbose = FALSE)
Expand Down
4 changes: 2 additions & 2 deletions R/mod_popExp_ui.R
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Expand Up @@ -10,7 +10,7 @@
#'
#' @import shiny
#' @importFrom plotly plotlyOutput
#' @importFrom IDEAFilter shiny_data_filter_ui
#' @importFrom IDEAFilter shiny_data_filter_ui IDEAFilter_ui

@AARON-CLARK AARON-CLARK Aug 21, 2023

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Is shiny_data_filter_ui still required?

Suggested change
#' @importFrom IDEAFilter shiny_data_filter_ui IDEAFilter_ui
#' @importFrom IDEAFilter IDEAFilter_ui

#'
#' @family popExp Functions
#' @noRd
Expand Down Expand Up @@ -46,7 +46,7 @@ mod_popExp_ui <- function(id, label = "Population Explorer"){
, value = FALSE)),
div(id = "pop_cic_filter_df", selectInput(ns("filter_df"),"Filter on Variable(s) in a loaded ADaM",
multiple = TRUE, choices = "ADSL", selected = "ADSL") ),
div(id = "pop_cic_data_filter", IDEAFilter::shiny_data_filter_ui(ns("data_filter"))))
div(id = "pop_cic_data_filter", IDEAFilter::IDEAFilter_ui(ns("data_filter"))))
),

div(id = "pop_cic_chart_type",
Expand Down
4 changes: 2 additions & 2 deletions R/mod_tableGen.R
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Expand Up @@ -4,7 +4,7 @@
#' @param datafile all uploaded data files from the dataImport module
#' @param filePaths NULL
#'
#' @importFrom IDEAFilter shiny_data_filter
#' @importFrom IDEAFilter shiny_data_filter IDEAFilter

@AARON-CLARK AARON-CLARK Aug 21, 2023

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is shiny_data_filter still required?

Suggested change
#' @importFrom IDEAFilter shiny_data_filter IDEAFilter
#' @importFrom IDEAFilter IDEAFilter

#' @importFrom rlang sym
#' @importFrom rlang !!
#' @importFrom rlang call2
Expand Down Expand Up @@ -180,7 +180,7 @@ mod_tableGen_server <- function(input, output, session, datafile = reactive(NULL
})

# create a reactive for the data with filters applied
filtered_data <- callModule(IDEAFilter::shiny_data_filter, "data_filter", data = processed_data, verbose = FALSE)
filtered_data <- IDEAFilter::IDEAFilter("data_filter", data = processed_data, verbose = FALSE)

# apply filters from selected dfs to tg data to create all data
all_data <- reactive({suppressMessages(bds_data() %>% semi_join(filtered_data()))})
Expand Down
4 changes: 2 additions & 2 deletions R/mod_tableGen_ui.R
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
#'
#'
#' @import shiny
#' @importFrom IDEAFilter shiny_data_filter_ui
#' @importFrom IDEAFilter shiny_data_filter_ui IDEAFilter_ui

@AARON-CLARK AARON-CLARK Aug 21, 2023

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Is shiny_data_filter_ui still required?

Suggested change
#' @importFrom IDEAFilter shiny_data_filter_ui IDEAFilter_ui
#' @importFrom IDEAFilter IDEAFilter_ui

#' @importFrom tippy tippy
#' @importFrom gt gt_output
#'
Expand Down Expand Up @@ -49,7 +49,7 @@ mod_tableGen_ui <- function(id){
tags$div(id = 'demo', class="collapse",
selectInput(ns("filter_df"),"Filter on Variable(s) in a loaded ADaM",
multiple = TRUE, choices = NULL, selected = NULL),
IDEAFilter::shiny_data_filter_ui(ns("data_filter"))
IDEAFilter::IDEAFilter_ui(ns("data_filter"))
))))),
wellPanel(
fluidRow(
Expand Down
81 changes: 34 additions & 47 deletions renv.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
"Package": "BiocManager",
"Version": "1.30.20",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Hash": "a7fca16a50b6ef7771b49d636dd54b57",
"Requirements": []
},
Expand Down Expand Up @@ -89,10 +89,15 @@
},
"IDEAFilter": {
"Package": "IDEAFilter",
"Version": "0.1.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "710e9b55aed4449b06ea1ab403dd0899",
"Version": "0.1.3.9008",
"Source": "GitHub",
"RemoteType": "github",
"RemoteHost": "api.github.com",
"RemoteRepo": "IDEAFilter",
"RemoteUsername": "Biogen-Inc",
"RemoteRef": "devel",
"RemoteSha": "a917cd33539efdc06dafc5713582951ffb44c596",
"Hash": "2501b36f26e192d194dba37869c9cb0a",
"Requirements": [
"RColorBrewer",
"crayon",
Expand Down Expand Up @@ -125,7 +130,7 @@
"Package": "R6",
"Version": "2.5.1",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "470851b6d5d0ac559e9d01bb352b4021",
"Requirements": []
},
Expand Down Expand Up @@ -172,7 +177,7 @@
"Package": "askpass",
"Version": "1.1",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "e8a22846fff485f0be3770c2da758713",
"Requirements": [
"sys"
Expand Down Expand Up @@ -372,7 +377,7 @@
"Package": "clipr",
"Version": "0.8.0",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "3f038e5ac7f41d4ac41ce658c85e3042",
"Requirements": []
},
Expand Down Expand Up @@ -449,7 +454,7 @@
"Package": "credentials",
"Version": "1.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "93762d0a34d78e6a025efdbfb5c6bb41",
"Requirements": [
"askpass",
Expand Down Expand Up @@ -517,7 +522,7 @@
"Package": "desc",
"Version": "1.4.2",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21",
"Requirements": [
"R6",
Expand Down Expand Up @@ -715,7 +720,7 @@
"Package": "ggcorrplot",
"Version": "0.1.4",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Hash": "463c9147c97479678b40bbf621a10635",
"Requirements": [
"ggplot2",
Expand Down Expand Up @@ -783,7 +788,7 @@
"Package": "glue",
"Version": "1.6.2",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "4f2596dfb05dac67b9dc558e5c6fba2e",
"Requirements": []
},
Expand Down Expand Up @@ -814,7 +819,7 @@
"Package": "graphql",
"Version": "1.5.1",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "dbaea71ccb07059f40ea9a739cc72279",
"Requirements": [
"Rcpp",
Expand Down Expand Up @@ -1127,7 +1132,7 @@
"Package": "magrittr",
"Version": "2.0.3",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "7ce2733a9826b3aeb1775d56fd305472",
"Requirements": []
},
Expand All @@ -1146,7 +1151,7 @@
"Package": "mgcv",
"Version": "1.8-41",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Hash": "6b3904f13346742caa3e82dd0303d4ad",
"Requirements": [
"Matrix",
Expand All @@ -1157,7 +1162,7 @@
"Package": "mime",
"Version": "0.12",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "18e9c28c1d3ca1560ce30658b22ce104",
"Requirements": []
},
Expand Down Expand Up @@ -1202,14 +1207,6 @@
"askpass"
]
},
"packrat": {
"Package": "packrat",
"Version": "0.9.1",
"Source": "Repository",
"Repository": "RSPM",
"Hash": "481428983c19a7c443f7ea1beff0a2de",
"Requirements": []
},
"pander": {
"Package": "pander",
"Version": "0.6.5",
Expand Down Expand Up @@ -1426,7 +1423,13 @@
"Package": "ps",
"Version": "1.7.2",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"RemoteType": "standard",
"RemotePkgRef": "ps",
"RemoteRef": "ps",
"RemoteRepos": "https://packagemanager.rstudio.com/cran/2023-03-01",
"RemotePkgPlatform": "i386+x86_64-w64-mingw32",
"RemoteSha": "1.7.2",
"Hash": "68dd03d98a5efd1eb3012436de45ba83",
"Requirements": []
},
Expand Down Expand Up @@ -1459,7 +1462,7 @@
"Package": "rappdirs",
"Version": "0.3.3",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "5e3c5dc0b071b21fa128676560dbe94d",
"Requirements": []
},
Expand Down Expand Up @@ -1626,7 +1629,7 @@
"Package": "rlang",
"Version": "1.0.6",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "4ed1f8336c8d52c3e750adcdc57228a7",
"Requirements": []
},
Expand Down Expand Up @@ -1676,26 +1679,10 @@
"Package": "rprojroot",
"Version": "2.0.3",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "1de7ab598047a87bba48434ba35d497d",
"Requirements": []
},
"rsconnect": {
"Package": "rsconnect",
"Version": "0.8.29",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "fe178fc15af80952f546aafedf655b36",
"Requirements": [
"curl",
"digest",
"jsonlite",
"openssl",
"packrat",
"rstudioapi",
"yaml"
]
},
"rstudioapi": {
"Package": "rstudioapi",
"Version": "0.14",
Expand Down Expand Up @@ -1789,7 +1776,7 @@
"Package": "shinyTime",
"Version": "1.0.3",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "CRAN",
"Hash": "836c3464fb0f2ea865ed4c35dcdc1eda",
"Requirements": [
"htmltools",
Expand Down Expand Up @@ -2093,7 +2080,7 @@
"Package": "usethis",
"Version": "2.1.6",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "a67a22c201832b12c036cc059f1d137d",
"Requirements": [
"cli",
Expand Down Expand Up @@ -2216,7 +2203,7 @@
"Package": "withr",
"Version": "2.5.0",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "RSPM",
"Hash": "c0e49a9760983e81e55cdd9be92e7182",
"Requirements": []
},
Expand Down