Takes figures created using the make figure functions and appends those figures to the specified report. While it takes all report types, it should act as a pass through for "xlsx"
Usage
nca_append_report_figs(
rpt = NULL,
mfres = list(),
rpttype = "docx",
fig_id = paste0("fig_", abs(rnorm(1))),
fig_desc = "Description of figure",
fig_height = 7,
fig_width = 6,
fig_start = c(0.07, 0.3),
fig_stop = c(0.93, 0.99),
text_format = "text",
caption_single = "A figure.",
caption_multiple = "Figure ===FIGNUM=== of ===FIGTOT===.",
title_single = "A figure title.",
title_multiple = "A figure title ===FIGNUM=== of ===FIGTOT===.",
sub_title_single = "Figure sub titles.",
sub_title_multiple = "Figure sub titles ===FIGNUM=== of ===FIGTOT===.",
flag_map = list()
)Arguments
- rpt
Reporting object (onbrand object for "pptx" and "docx" rpttypes and a list for "xlsx")
- mfres
Output from make figure functions (e.g.
mk_figure_ind_obs())- rpttype
Type of report either ("docx" (default), "pptx", or "xlsx")
- fig_id
Unique figure ID
- fig_desc
Verbose description of the figure
- fig_height
Word report figure height in inches (7)
- fig_width
Word report figure width in inches (6)
- fig_start
In PowerPoint the x and y locations to start relateive to the upper left of the slide.
- fig_stop
In PowerPoint the x and y locations to stop relateive to the upper left of the slide.
- text_format
How to format text ("md" for markdown or "text" for regular text (default))
- caption_single
Caption for a single figure
- caption_multiple
Caption for a multiple figures with optional placeholders for the total number of figures (
===FIGTOT===) and the current figure number (===FIGNUM===).- title_single
Title for a single figure
- title_multiple
title for a multiple figures with optional placeholders for the total number of figures (
===FIGTOT===) and the current figure number (===FIGNUM===).- sub_title_single
Title for a single figure
- sub_title_multiple
title for a multiple figures with optional placeholders for the total number of figures (
===FIGTOT===) and the current figure number (===FIGNUM===).- flag_map
List with flag mapping details.
Value
list with the following elements
isgood: Boolean indicating the exit status of the function.
msgs: Messages to be passed back to the user.
obnd: Report with tables added.
Examples
if(interactive()){
# original file: inst/templates/ruminate.R
library(formods)
library(ruminate)
# These are suggested packages
library(shinydashboard)
#library(ggpubr)
#library(plotly)
#library(shinybusy)
library(prompter)
#library(utils)
tags$style("@import url(https://use.fontawesome.com/releases/v6.4.0/css/all.css);")
# You can copy these locally and customize them for your own needs. Simply
# change the assignment to the local copy you've modified.
formods.yaml = system.file(package="formods", "templates", "formods.yaml")
ASM.yaml = system.file(package="formods", "templates", "ASM.yaml")
UD.yaml = system.file(package="formods", "templates", "UD.yaml")
DW.yaml = system.file(package="formods", "templates", "DW.yaml")
FG.yaml = system.file(package="formods", "templates", "FG.yaml")
NCA.yaml = system.file(package="ruminate", "templates", "NCA.yaml")
# Name of file to indicate we need to load testing data
ftmptest = file.path(tempdir(), "ruminate.test")
# Making sure that the deployed object is created
if(!exists("deployed")){
deployed = FALSE
}
# If the DEPLOYED file marker existrs we set deployed to TRUE
if(file.exists("DEPLOYED")){
deployed = TRUE
}
# # Making sure that the run_dev object is created
# if(file.exists(file.path(tempdir(), "RUMINTE_DEVELOPMENT"))){
# run_dev = TRUE
# }else{
# run_dev = FALSE
# }
# If the SETUP.R file exists we source it
if(file.exists("SETUP.R")){
source("SETUP.R")
}
CSS <- "
.wrapfig {
float: right;
shape-margin: 20px;
margin-right: 20px;
margin-bottom: 20px;
}
"
#https://fontawesome.com/icons?from=io
logo_url =
"https://raw.githubusercontent.com/john-harrold/ruminate/main/man/figures/logo.png"
data_url =
"https://github.com/john-harrold/formods/raw/master/inst/test_data/TEST_DATA.xlsx"
run_url =
"https://runruminate.ubiquity.tools/"
use_url =
"https://useruminate.ubiquity.tools/"
main_url =
"https://ruminate.ubiquity.tools/"
issue_url =
"https://github.com/john-harrold/ruminate/issues"
intro_text = tags$p(
"Ruminate is a shiny module for pharmacometric data processing,
visualization, and analysis. It consists of separate shiny modules that
provide interfaces into common R packages and provides the underlying code.
This is done to facilitate usage of those packages and to provide reproducible
analyses." ,
tags$li( "To find out more visit ",
tags$a("ruminate.ubiquity.tools", href=main_url),""),
tags$li( "To give it a try you can download a test dataset ",
tags$a("here", href=data_url),""),
tags$li( "Go to ",
tags$a("useruminate.ubiquity.tools", href=use_url)," for a video
demonstrating how to use ruminate"),
tags$li( "If you run into any problems, have questions, or want a feature please
visit the ",
tags$a("issues", href=issue_url)," page")
)
ui <- shinydashboard::dashboardPage(
skin="black",
shinydashboard::dashboardHeader(title="ruminate"),
shinydashboard::dashboardSidebar(
shinydashboard::sidebarMenu(
shinydashboard::menuItem("Load/Save",
tabName="loadsave",
icon=icon("arrow-down-up-across-line")) ,
shinydashboard::menuItem("Transform Data", tabName="wrangle", icon=icon("shuffle")),
shinydashboard::menuItem("Visualize", tabName="plot", icon=icon("chart-line")),
shinydashboard::menuItem("NCA", tabName="nca", icon=icon("chart-area")),
shinydashboard::menuItem("App Info", tabName="sysinfo", icon=icon("book-medical"))
)
),
shinydashboard::dashboardBody(
tags$head(
tags$style(HTML(CSS))
),
shinydashboard::tabItems(
shinydashboard::tabItem(tabName="nca",
shinydashboard::box(title="Non-Compartmental Analysis", width=12,
fluidRow( prompter::use_prompt(),
column(width=12,
htmlOutput(NS("NCA", "NCA_ui_compact")))))
),
shinydashboard::tabItem(tabName="loadsave",
# shinydashboard::box(title=NULL, width=12,
shinydashboard::tabBox(
width = 12,
title = NULL,
shiny::tabPanel(id="load_data",
title=tagList(shiny::icon("file-arrow-up"),
"Load Data"),
fluidRow(
column(width=6,
div(style="display:inline-block;width:100%",
htmlOutput(NS("UD", "ui_ud_load_data"))),
htmlOutput(NS("UD", "ui_ud_clean")),
htmlOutput(NS("UD", "ui_ud_select_sheets")),
htmlOutput(NS("UD", "ui_ud_workflows")),
htmlOutput(NS("UD", "ui_ud_text_load_result"))),
column(width=6,
tags$p(
tags$img(
class = "wrapfig",
src = logo_url,
width = 150,
alt = "formods logo" ),
intro_text
))
),
fluidRow(
column(width=12,
div(style="display:inline-block;vertical-align:top",
htmlOutput(NS("UD", "ui_ud_data_preview")))
))
),
shiny::tabPanel(id="save_state",
title=tagList(shiny::icon("arrow-down-up-across-line"),
"Save or Load Analysis"),
fluidRow(
column(width=5,
div(style="display:inline-block;vertical-align:top",
htmlOutput(NS("ASM", "ui_asm_compact"))
))
)
)
)
# ),
),
shinydashboard::tabItem(tabName="wrangle",
shinydashboard::box(title="Transform and Create Views of Your Data", width=12,
fluidRow(
column(width=12,
htmlOutput(NS("DW", "DW_ui_compact")))))
),
shinydashboard::tabItem(tabName="plot",
shinydashboard::box(title="Visualize Data", width=12,
htmlOutput(NS("FG", "FG_ui_compact")))),
shinydashboard::tabItem(tabName="sysinfo",
# box(title="System Details", width=12,
shinydashboard::tabBox(
width = 12,
title = NULL,
shiny::tabPanel(id="sys_packages",
title=tagList(shiny::icon("box-open"),
"Installed Packages"),
htmlOutput(NS("ASM", "ui_asm_sys_packages"))
),
shiny::tabPanel(id="sys_modules",
title=tagList(shiny::icon("cubes"),
"Loaded Modules"),
htmlOutput(NS("ASM", "ui_asm_sys_modules"))
),
shiny::tabPanel(id="sys_log",
title=tagList(shiny::icon("clipboard-list"),
"Log"),
verbatimTextOutput(NS("ASM", "ui_asm_sys_log"))
),
shiny::tabPanel(id="sys_options",
title=tagList(shiny::icon("sliders"),
"R Options"),
htmlOutput(NS("ASM", "ui_asm_sys_options"))
),
shiny::tabPanel(id="sys_deps",
title=tagList(shiny::icon("box-open"),
"Dependencies"),
htmlOutput("ui_sys_deps")
)
# )
))
)
)
)
# Main app server
server <- function(input, output, session) {
# Empty reactive object to track and react to
# changes in the module state outside of the module
react_FM = reactiveValues()
# Module IDs and the order they are needed for code generation
mod_ids = c("UD", "DW", "FG", "NCA", "MB")
# If the ftmptest file is present we load test data
if(file.exists(ftmptest)){
sources = c(system.file(package="formods", "preload", "ASM_preload.yaml"),
system.file(package="formods", "preload", "UD_preload.yaml"),
system.file(package="formods", "preload", "FG_preload.yaml"),
system.file(package="formods", "preload", "DW_preload.yaml"),
system.file(package="ruminate", "preload", "NCA_preload.yaml"))
res = FM_app_preload(session=session, sources=sources)
# Otherwise we look for a preload file and load that if it exists
} else if(file.exists("preload.yaml")){
shinybusy::show_modal_spinner(text="Preloading analysis, be patient", session=session)
res = FM_app_preload(session=session, sources="preload.yaml")
shinybusy::remove_modal_spinner(session = session)
}
# Module servers
formods::ASM_Server( id="ASM",
deployed = deployed,
react_state = react_FM,
FM_yaml_file = formods.yaml,
MOD_yaml_file = ASM.yaml,
mod_ids = mod_ids)
formods::UD_Server( id ="UD", id_ASM = "ASM",
deployed = deployed,
react_state = react_FM,
MOD_yaml_file = UD.yaml,
FM_yaml_file = formods.yaml)
formods::DW_Server( id="DW", id_ASM = "ASM",
id_UD = "UD",
deployed = deployed,
react_state = react_FM,
MOD_yaml_file = DW.yaml,
FM_yaml_file = formods.yaml)
formods::FG_Server( id="FG", id_ASM = "ASM",
id_UD = "UD", id_DW = "DW",
deployed = deployed,
react_state = react_FM,
MOD_yaml_file = FG.yaml,
FM_yaml_file = formods.yaml)
ruminate::NCA_Server(id ="NCA", id_ASM = "ASM",
id_UD = "UD", id_DW = "DW",
deployed = deployed,
react_state = react_FM,
MOD_yaml_file = NCA.yaml,
FM_yaml_file = formods.yaml)
output$ui_sys_deps = renderUI({
pcf = formods_check(verbose = FALSE)
pcr = ruminate_check(verbose = FALSE)
dep_sum = NULL
if(!is.null(pcf[["found_pkgs"]])){
dep_sum = rbind(dep_sum,
data.frame(
Package = "formods",
Dependency = pcf[["found_pkgs"]],
Status = "found"
))
}
if(!is.null(pcf[["missing_pkgs"]])){
dep_sum = rbind(dep_sum,
data.frame(
Package = "formods",
Dependency = pcf[["missing_pkgs"]],
Status = "missing"
))
}
if(!is.null(pcr[["found_pkgs"]])){
dep_sum = rbind(dep_sum,
data.frame(
Package = "ruminate",
Dependency = pcr[["found_pkgs"]],
Status = "found"
))
}
if(!is.null(pcr[["missing_pkgs"]])){
dep_sum = rbind(dep_sum,
data.frame(
Package = "ruminate",
Dependency = pcr[["missing_pkgs"]],
Status = "missing"
))
}
uiele = DT::datatable(dep_sum)
uiele})
}
shinyApp(ui, server)
}