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Enhancement: Refactor Visualisation Tab #136

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merged 11 commits into from
Dec 19, 2024
Merged

Enhancement: Refactor Visualisation Tab #136

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ab6996f
refactor: modularise visuals section
js3110 Nov 22, 2024
617850e
refactor: initial partial change to bslib format
js3110 Nov 22, 2024
5684c04
add bslib to NAMESPACE
js3110 Nov 25, 2024
2b3c248
refactor: working bslib format
js3110 Nov 25, 2024
bc32d8a
lint: fix lint issues
js3110 Nov 25, 2024
7f330ef
refactor: update indentation and remove dead code
js3110 Dec 16, 2024
f7100eb
resolve conflicts
js3110 Dec 16, 2024
cc79640
refactor: better indentation, fixed lintr issues
m-kolomanski Dec 17, 2024
8a26d56
fix: final lintr fixes
js3110 Dec 17, 2024
31ec335
add logs and clean up labels
js3110 Dec 18, 2024
9c99cc8
fix: lint
js3110 Dec 18, 2024
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4 changes: 4 additions & 0 deletions inst/shiny/global.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,8 @@ source("modules/tab_data.R")
source("modules/slope_selector.R")

source("functions/partial_auc_input.R")

source("modules/tab_visuals.R")

source("functions/mapping_selectize_inputs.R")

146 changes: 106 additions & 40 deletions inst/shiny/modules/column_mapping.R
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Original file line number Diff line number Diff line change
Expand Up @@ -46,27 +46,40 @@ column_mapping_ui <- function(id) {
tagList(
h3("Data Mapping"),
br(),
"The following columns are required for data analysis.
Please ensure each of these columns has been assigned
a corresponding column from your dataset",
p(
"The following columns are required for data analysis. Please ensure each of these columns",
" has been assigned a corresponding column from your dataset"
),
br(),
fluidRow(
h4("Group Identifiers"),
column(12,
tooltip(
selectizeInput(ns("select_STUDYID"), "STUDYID",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_STUDYID"),
"STUDYID",
choices = NULL,
options = list(placeholder = "Select Column")
),
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"Select Study ID Column"
),
tooltip(
selectizeInput(ns("select_USUBJID"), "USUBJID",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_USUBJID"),
"USUBJID",
choices = NULL,
options = list(placeholder = "Select Column")
),
"Unique subject identifier."
),
tooltip(
selectizeInput(ns("select_Grouping_Variables"), "Grouping Variables",
choices = NULL, multiple = TRUE,
options = list(placeholder = "Select Column(s)")),
selectizeInput(
ns("select_Grouping_Variables"),
"Grouping Variables",
choices = NULL,
multiple = TRUE,
options = list(placeholder = "Select Column(s)")
),
"Select the additional column(s) that will be used to group the data
for tables, listings and graphs. E.g. Treatment Arm, Age, Sex, Race"
)
Expand All @@ -76,18 +89,29 @@ a corresponding column from your dataset",
h4("Sample Variables"),
column(12,
tooltip(
selectizeInput(ns("select_ANALYTE"), "ANALYTE",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_ANALYTE"),
"ANALYTE",
choices = NULL,
options = list(placeholder = "Select Column")
),
"Analyte"
),
tooltip(
selectizeInput(ns("select_PCSPEC"), "PCSPEC",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_PCSPEC"),
"PCSPEC",
choices = NULL,
options = list(placeholder = "Select Column")
),
"Matrix"
),
tooltip(
selectizeInput(ns("select_AVAL"), "AVAL",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_AVAL"), "AVAL",
choices = NULL,
options = list(placeholder = "Select Column")
),
"Analysis value in numeric format."
)
)
Expand All @@ -96,24 +120,38 @@ a corresponding column from your dataset",
h4("Dose Variables"),
column(12,
tooltip(
selectizeInput(ns("select_DOSNO"), "DOSNO",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_DOSNO"),
"DOSNO",
choices = NULL, options = list(placeholder = "Select Column")
),
"Numeric format."
),
tooltip(
selectizeInput(ns("select_ROUTE"), "ROUTE",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_ROUTE"),
"ROUTE",
choices = NULL,
options = list(placeholder = "Select Column")
),
"Route of administration, stating either 'intravascular' or 'extravascular'."
),
tooltip(
selectizeInput(ns("select_DOSEA"), "DOSEA",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_DOSEA"),
"DOSEA",
choices = NULL,
options = list(placeholder = "Select Column")
),
"Actual Dose amount in numeric format."
),
tooltip(
selectizeInput(ns("select_ADOSEDUR"), "ADOSEDUR",
choices = c("Select Column" = "", "NA"),
options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_ADOSEDUR"),
"ADOSEDUR",
choices = c("Select Column" = "", "NA"),
options = list(placeholder = "Select Column")
),
"Duration of dose administration. Only required for infusion studies,
otherwise select NA"
)
Expand All @@ -123,23 +161,39 @@ otherwise select NA"
h4("Time Variables"),
column(12,
tooltip(
selectizeInput(ns("select_AFRLT"), "AFRLT",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_AFRLT"),
"AFRLT",
choices = NULL,
options = list(placeholder = "Select Column")
),
"Numeric format"
),
tooltip(
selectizeInput(ns("select_ARRLT"), "ARRLT",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_ARRLT"),
"ARRLT",
choices = NULL,
options = list(placeholder = "Select Column")
),
"Numeric format"
),
tooltip(
selectizeInput(ns("select_NFRLT"), "NFRLT",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_NFRLT"),
"NFRLT",
choices = NULL,
options = list(placeholder = "Select Column")
),
"Numeric format"
),
tooltip(
selectizeInput(ns("select_NRRLT"), "NRRLT",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_NRRLT"),
"NRRLT",
choices = NULL,
options = list(placeholder = "Select Column")
),
"Numeric format"
)
)
Expand All @@ -148,20 +202,32 @@ otherwise select NA"
h4("Unit Variables"),
column(12,
tooltip(
selectizeInput(ns("select_AVALU"), "AVALU",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_AVALU"),
"AVALU",
choices = NULL,
options = list(placeholder = "Select Column")
),
"Unit of analysis value. If a column is not available, type and select the unit
used in the dataset from the manual units."
),
tooltip(
selectizeInput(ns("select_DOSEU"), "DOSEU",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_DOSEU"),
"DOSEU",
choices = NULL,
options = list(placeholder = "Select Column")
),
"Unit of dose amount. If a column is not available, type and select the unit
used in the dataset from the manual units"
),
tooltip(
selectizeInput(ns("select_RRLTU"), "RRLTU",
choices = NULL, options = list(placeholder = "Select Column")),
selectizeInput(
ns("select_RRLTU"),
"RRLTU",
choices = NULL,
options = list(placeholder = "Select Column")
),
"Unit of time. If a column is not available, type and select the unit
used in the dataset from the manual units"
)
Expand Down Expand Up @@ -234,7 +300,7 @@ column_mapping_server <- function(id, data, manual_units, on_submit) {
}

# Extract and store the "Grouping Variables" column
grouping_variables(selected_cols[["Group Identifiers"]][["Grouping Variables"]])
grouping_variables(input$select_Grouping_Variables)

# Remove "Grouping Variables" from selected columns to prevent renaming
selected_cols[["Group Identifiers"]] <- selected_cols[["Group Identifiers"]][
Expand Down
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