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inst/GerminaQuant/ui.R
In GerminaR: Indices and Graphics for Assess Seed Germination Process
# -------------------------------------------------------------------------
# GerminaR-----------------------------------------------------------------
# -------------------------------------------------------------------------
#> open https://flavjack.github.io/GerminaR/
#> open https://flavjack.shinyapps.io/germinaquant/
#> author .: Flavio Lozano-Isla (lozanoisla.com)
#> date .: 2021-10-10
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
# packages ----------------------------------------------------------------
# -------------------------------------------------------------------------
#> devtools::install_github("flavjack/GerminaR")
source("msgs.R")
suppressPackageStartupMessages({source("pkgs.R")})
# app ---------------------------------------------------------------------
# -------------------------------------------------------------------------
shinyUI(dashboardPage(skin = "green",
dashboardHeader(title = "GerminaQuant • app",
tags$li(class="dropdown", tags$a(href="https://github.com/sponsors/flavjack", icon("heart"), target="_blank")),
tags$li(class="dropdown", tags$a(href="https://germinar.inkaverse.com/news/" , paste("GerminaR", packageVersion('GerminaR')), target="_blank"))
),
# Sider -------------------------------------------------------------------
dashboardSidebar(
sidebarMenu(
menuItem("Presentacion", tabName = "intro", icon = icon("home")),
menuItem("Fieldbook", tabName = "fieldbook", icon = icon("file-alt")),
menuItem("Germination", tabName = "germination", icon = icon("seedling")),
menuItem("Exploratory", tabName = "outlier", icon = icon("search")),
menuItem("Statistics", tabName = "stat", icon = icon("chart-pie")),
menuItem("Graphics", tabName = "graph", icon = icon("tint")),
menuItem("InTime", tabName = "germint", icon = icon("hourglass")),
menuItem("Tools", tabName = "tools", icon = icon("wrench"))
)
),
dashboardBody(
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "custom.css")
),
tags$head(includeHTML(("www/analytics.html"))),
tags$head(tags$link(rel="shortcut icon", href="https://flavjack.github.io/GerminaR/reference/figures/logo.png")),
meta() %>%
meta_social(
title = "GerminaR",
description = "Indices and Graphics for Assess Seed Germination Process",
url = "https://flavjack.shinyapps.io/germinaquant/",
image = "https://flavjack.github.io/GerminaR/reference/figures/logo.png",
image_alt = "GerminaR"
),
tabItems(
# presentation ------------------------------------------------------------
# -------------------------------------------------------------------------
tabItem(tabName = "intro",
shiny::fluidRow(
box(
title = "GerminaQuant",
width = 3,
status = "primary",
solidHeader = T,
HTML('
<p>
<strong>GerminaQuant</strong> for R is a web application based in R,
you can use the app in your desktop installing the <em><strong>GerminaR</strong></em> package:
</p>
Install the package in the R console
<br>
<code>install.packages("GerminaR")</code>
<br>
<br>
For use the interactive app
<br>
<code>GerminaR::GerminaQuant()</code>
<br>
<br>
<div id=footer style="width:100%; margin:auto;">
<div style="display:inline-block; width:48%">
<p style="text-align:center">
<a target="_blank" href="https://flavjack.github.io/GerminaR/"><img src="https://pkgdown.r-lib.org/reference/figures/logo.png" style="height:75px" title="GerminaR" alt="GerminaR"></a>
<span style="display:block;"><small>GerminaR</small></span>
</p></div>
<div style="display:inline-block; width:48%">
<p style="text-align:center">
<a target="_blank" href="https://youtube.com/playlist?list=PLSQMdOu57lj9QUoA6JLuv0nBTYacuyrbg"><img src="https://lozanoisla.com/img/youtube.png" style="height:70px" title="Demo" alt="Demo"></a>
<span style="display:block;"><small>Demo</small></span>
</p></div>
</div>
')
),
box(width = 5,
title = "Characteristics",
status = "danger",
solidHeader = T,
p("GerminaQuant for R is based in GerminaR R package, a highly interactive data analysis platform for germination analysis,
tool develpment for the Plant Physiology Laboratory (UFPE).
It is result of a continuous effort to improve data collection, quality, analysis and open access publication.
The recent iteration simultaneously also represents efforts to unify best practices from experiences in germination data management.
One of the main new characteristics of the current software development platform established is the web-based interface
which provides also a highly interactive environment. It could be used both online and offline and on desktop as well as tablets and laptops.
The aime is support the broader research community working on all aspects with germination studies."),
HTML("
<h5><b>Features</b></h5>
<p>
<ol>
<li> Allow calculate the principal germination indices.</li>
<li> Statistical analysis for germination.</li>
<li> Easy way to plot the results.</li>
</ol>
</p>
")
),
box(
title = "Package Info",
width = 4,
status = "success",
solidHeader = T,
p(strong("Publication")),
HTML('<p><strong>Flavio Lozano-Isla</strong>; <strong>Omar E. Benites-Alfaro</strong>, and<strong> Marcelo F. Pompelli</strong>. <strong>2019</strong>.
GerminaR: An R package for germination analysis with the interactive web application “GerminaQuant for R.”
Ecological Research 34(2): 339–346. doi: <a href="http://doi.org/10.1111/1440-1703.1275">doi.org/10.1111/1440-1703.1275</a>.</p>'),
br(),
HTML('
<div id=footer style="width:100%; margin:auto;">
<div style="display:inline-block; width:32%">
<p style="text-align:center">
<a target="_blank" href="https://github.com/Flavjack/GerminaR"><img src="https://github.githubassets.com/images/modules/logos_page/Octocat.png" style="height:80px" title="Github" alt="Github"></a>
<span style="display:block;"><small>Github</small></span>
</p></div>
<div style="display:inline-block; width:32%">
<p style="text-align:center">
<a target="_blank" href="https://CRAN.R-project.org/package=GerminaR"><img src="https://flavjack.github.io/GerminaR/reference/figures/logo.png" style="height:80px" title="R cran" alt="GerminaR"></a>
<span style="display:block;"><small>CRAN</small></span>
</p></div>
<div style="display:inline-block; width:32%">
<p style="text-align:center">
<a target="_blank" href="https://flavjack.shinyapps.io/germinaquant/"><img src="https://flavjack.github.io/GerminaR/img/GerminaQuant.png" style="height:80px" title="GerminaQuant" alt="GerminaQuant for R"></a>
<span style="display:block;"><small>GerminaQuant</small></span>
</p></div>
</div>
'),
hr(),
HTML('<p>If you have any question, comment or suggestion you can write at <a href="mailto:flavjack@gmail.com">flozano@lamolina.edu.pe</a></p>')
)
)
),
# fieldbook -------------------------------------------------------------
tabItem(tabName = "fieldbook",
box(
status = "info",
width = 12,
background = "black"
, height = "120px",
column(width = 6,
h4(icon("google"), "Google SpreadSheet (URL)", width = "100%"),
textInput("import_gsheet",
label = NULL ,
width = "100%",
value = "https://docs.google.com/spreadsheets/d/1QziIXGOwb8cl3GaARJq6Ez6aU7vND_UHKJnFcAKx0VI/edit#gid=137089581")
),
column(width = 4,
h4(icon("file-excel"), "Excel file (.xlsx)", width = "100%"),
fileInput('import_excel'
, multiple = FALSE
, label = NULL
, accept = c(".xlsx")
)
),
column(width = 1,
h4("Sheet", width = "100%"),
numericInput("sheetdt", label = NULL, value = 1, step = 1, min = 1)
),
column(width = 1,
h4( "Update", width = "100%"),
actionButton(inputId = "reload", label = "", icon("sync"), width = "100%")
)
),
shiny::fluidRow(
box(
status = "danger",
solidHeader = T,
width = 10,
htmlOutput("data_viewer")
),
# Germination parameters --------------------------------------------------
box(
status = "danger",
solidHeader = T,
width = 2,
title = 'Parameters',
textInput("SeedN", label = strong("Seeds (column name)"), value = "seeds"),
textInput("evalName", label = strong("Evaluations (prefix)"), value = "D")
)
)
),
# Germination analisys ----------------------------------------------------
tabItem(tabName = "germination",
shiny::fluidRow(
box(width = 12,
DT::dataTableOutput("summary"),
br(),
actionButton(inputId= 'indicesLink', label = "Indices info"
, icon = icon("seedling")
, onclick ="window.open('https://germinar.inkaverse.com/articles/introduction.html', '_blank')"
)
)
)
),
# outliers ----------------------------------------------------------------
tabItem(tabName = "outlier",
box(width = 6, background = "black",
column(width = 4,
uiOutput("bpy")
),
column(width = 4,
uiOutput("bpx")
),
column(width = 4,
uiOutput("bpz")
),
column(width = 4,
textInput(inputId ="bply", label = "Y label", value = "")
),
column(width = 4,
textInput(inputId ="bplx", label = "X label", value = "")
),
column(width = 4,
textInput(
inputId ="bplz",
label = "Legend label",
value = "")
)
),
box(width = 3, background = "black",
column(width = 6,
textInput(
inputId ="bpbrk"
, label = "Y limits"
, value = NULL
, placeholder = "0*100*20"
)
),
column(width = 6,
textInput(
inputId ="bprot"
, label = "X rotation"
, value = "0*0.5*0.5"
, placeholder = "angle*h*v"
)
),
column(width = 12,
textInput(
inputId ="bpopt"
, label = "Opt"
, placeholder = "extra layer"
)
)
),
box(width = 3, background = "black",
column(width = 6,
numericInput(
inputId ="bpwd"
, label = "Width (cm)"
, value = 20
, step = 2
)
),
column(width = 6,
numericInput(
inputId = "bphg"
, label = "Height (cm)"
, value = 10
, step = 2
)
),
column(width = 6,
numericInput(
inputId ="bprs"
, label = "Resolution (dpi)"
, value = 100
, step = 50
)
),
column(width = 6,
selectInput(
inputId = "bplg"
, label = "Legend"
, choices = c("top", "bottom", "left", "right", "none")
)
),
),
shiny::fluidRow(
box(width = 12,
div(imageOutput("boxplot"), align = "center")
)
)
),
# statistics -------------------------------------------------------------
tabItem(tabName = "stat",
shiny::fluidRow(
box(width = 5, background = "black",
column(width = 5,
radioButtons(inputId = "stat_model"
, label = "Model parameters"
, choices = c("auto", "manual")
, inline = TRUE
)
),
column(width = 7,
br(),
verbatimTextOutput("model_formula")
),
column(width = 12,
uiOutput("stat_response")
),
hr(),
conditionalPanel(
condition = "input.stat_model == 'auto'",
column(width = 8,
uiOutput("stat_factor")
),
column(width = 4,
uiOutput("stat_block")
),
),
conditionalPanel(
condition = "input.stat_model == 'manual'",
column(width = 12,
textInput(inputId = "stat_model_factors"
, label = "Experiment model factors"
, placeholder = "e.g. block + factor1*factor2"
)
),
),
column(width = 6,
uiOutput("stat_comparison")
),
column(width = 3,
numericInput("stsig",
label = "Significance",
value = 0.05,
min = 0,
max = 5,
step = 0.01)
),
column(width = 3,
selectInput("stmc",
label = "Type",
choices = c("tukey", "duncan", "snk"),
selected = "snk")
),
column(width = 12,
verbatimTextOutput("tbav")
),
column(width = 12,
DT::dataTableOutput("stat_summary")
)
),
box(width = 7,
box(title = "Summary table",
solidHeader = T,
width = 12,
collapsible = T,
collapsed = T,
status = "primary",
DT::dataTableOutput("mnc")
),
box(title = "Model diagnostic",
solidHeader = T,
width = 12,
collapsible = T,
collapsed = T,
status = "danger",
plotOutput("modelplots")
)
)
)
),
# graphics ----------------------------------------------------------------
# -------------------------------------------------------------------------
tabItem(tabName = "graph",
fluidRow(
column( width = 12,
box(width = 6, title = NULL, background = "blue",
column(width = 4,
textInput(
inputId ="plot_ylab",
label = "Y label")
),
column(width = 4,
textInput(inputId ="plot_xlab", label = "X label")
),
column(width = 4,
textInput(inputId ="plot_glab"
, label = "Group label")
),
column(width = 4,
HTML("<b>Model</b>"),
br(),
br(),
textOutput("graph_formula")
),
column(width = 4,
textInput(inputId ="plot_xbrakes"
, label = "X brake labels (,)")
),
column(width = 4,
textInput(inputId ="plot_gbrakes"
, label = "Group brake labels (,)")
),
),
box(width = 3, background = "black",
column(width = 6,
textInput(
inputId ="plot_ylimits"
, label = "Y limits"
, value = NULL
, placeholder = "0*100*20"
)
),
column(width = 6,
textInput(
inputId ="plot_xrotation"
, label = "X rotation"
, value = "0*0.5*0.5"
, placeholder = "angle*h*v"
)
),
column(width = 12,
textInput(
inputId ="plot_opt"
, label = "Opt"
, placeholder = "extra layer"
)
)
),
box(width = 3, background = "black",
column(width = 6,
numericInput(
inputId ="plot_width"
, label = "Width (cm)"
, value = 20
, step = 2
)
),
column(width = 6,
numericInput(
inputId = "plot_height"
, label = "Height (cm)"
, value = 10
, step = 2
)
),
column(width = 6,
numericInput(
inputId ="plot_res"
, label = "Resolution (dpi)"
, value = 100
, step = 50
)
),
column(width = 6,
selectInput(
inputId = "plot_legend"
, label = "Legend"
, choices = c("top"
, "bottom"
, "left"
, "right"
, "none")
)
),
),
shiny::fluidRow(
box(width = 10,
div(imageOutput("plotgr"), align = "center")
),
column(width = 2,
column(width = 12,
radioButtons(
inputId ="plot_type",
label = "Type",
choices = c("bar", "line"),
inline = TRUE
)
),
column(width = 12,
radioButtons(
inputId ="plot_color",
label = "Color",
choices = c("yes"
, "no" = "none"
),
inline = TRUE)
),
column(width = 12,
radioButtons(
inputId ="plot_sig",
label = "Significance",
choices = c("yes" = "sig"
, "no" = "none"
),
inline = TRUE)
),
column(width = 12,
radioButtons(
inputId ="plot_error",
label = "Error",
choices = c("ste"
, "std"
, "no" = "none"
),
inline = TRUE)
)
)
)
)
)
),
# Germination in time -----------------------------------------------------
# -------------------------------------------------------------------------
tabItem(tabName = "germint",
fluidRow(
column( width = 12,
box(width = 6, title = NULL, background = "blue",
column(width = 4,
textInput(
inputId ="intime_ylab",
label = "Y label"
, value = "Germination ('%')")
),
column(width = 4,
textInput(inputId ="intime_xlab"
, label = "X label"
, value = "Time")
),
column(width = 4,
textInput(inputId ="intime_glab"
, label = "Group label")
),
column(width = 4,
uiOutput('smvar')
),
column(width = 4,
# textInput(inputId ="intime_xbrakes"
# , label = "X brake labels (,)"
# )
),
column(width = 4,
textInput(inputId ="intime_gbrakes"
, label = "Group brake labels (,)")
),
),
box(width = 3, background = "black",
column(width = 6,
textInput(
inputId ="intime_ylimits"
, label = "Y limits"
, value = NULL
, placeholder = "0*100*20"
)
),
column(width = 6,
textInput(
inputId ="intime_xrotation"
, label = "X rotation"
, value = "0*0.5*0.5"
, placeholder = "angle*h*v"
)
),
column(width = 12,
textInput(
inputId ="intime_opt"
, label = "Opt"
, placeholder = "extra layer"
)
)
),
box(width = 3, background = "black",
column(width = 6,
numericInput(
inputId ="intime_width"
, label = "Width (cm)"
, value = 20
, step = 2
)
),
column(width = 6,
numericInput(
inputId = "intime_height"
, label = "Height (cm)"
, value = 10
, step = 2
)
),
column(width = 6,
numericInput(
inputId ="intime_res"
, label = "Resolution (dpi)"
, value = 100
, step = 50
)
),
column(width = 6,
selectInput(
inputId = "intime_legend"
, label = "Legend"
, choices = c("top"
, "bottom"
, "left"
, "right"
, "none")
)
),
),
shiny::fluidRow(
box(width = 10,
div(imageOutput("intime_plot"), align = "center")
),
column(width = 2,
column(width = 12,
radioButtons(
inputId ="intime_type",
label = "Type",
choices = c("percentage", "relative"),
selected = "percentage",
inline = F)
),
column(width = 12,
radioButtons(
inputId ="intime_color",
label = "Color",
choices = c("yes"
, "no" = "none"
),
inline = TRUE)
),
column(width = 12,
radioButtons(
inputId ="intime_error",
label = "Error",
choices = c("ste"
, "std"
, "no" = "none"
),
inline = TRUE)
)
)
)
)
)
),
# tools -------------------------------------------------------------------
tabItem(tabName = "tools", withMathJax(),
shiny::fluidRow(
box(width = 7,
title = "Osmotic potencial",
status = "primary",
solidHeader = T,
br(),
p("The osmotic potencial, can be measured directly with an osmometer, or it can be calculated from the solute concentration."),
hr(),
p("For a salt, you can use the van't Hoff relation: $$\\psi_s = -RTC_i$$ where: \\(R\\) is the gas constant (i.e. \\(0.0083 L/atm/mol/K\\)), \\(T\\) is the absolute temperature in degrees in Kelvin (\\(273.15^{o}C\\)),
\\(C\\) is the solute concentration in \\(mol*L^{-1}\\), and \\(i\\) is the dissociation constant of the salt. (i.e. \\(NaCl = 1.8, KCl = 1.8, CaCl_2 = 2.4, sacarose = 1\\)). The unit for \\(\\psi_s\\) is \\(MPa\\)"),
hr(),
p("For", em("PEG-6000"), "the osmotic potentials can be calculated as described by", a("Michel and Kaufmann (1973):", href = "http://www.plantphysiol.org/content/51/5/914.abstract", target="_blank"), "$$\\psi_s = -(1.18*10^{-2})C - (1.18*10^{-4})C^2 + (2.67*10^{-4})CT + (8.39*10^{-7})C^2T$$
where: \\(C\\) is the concentration of", em("PEG-6000"), "in \\(g*L^{-1}\\) and \\(T\\) is the temperature in degrees \\(^{o}C\\). The unit for \\(\\psi_s\\) is \\(bar (0.1 MPa)\\)."),
br()
),
box(
title = "Calculator",
status = "info",
solidHeader = T,
width = 5,
column(width = 12,
h2(textOutput("ops")),
tags$style(type="text/css", "#ops { height: 50px; width: 100%; text-align:center; font-size: 35px;}")
),
column(width = 12,
radioGroupButtons(
inputId = "tool_osmp",
status = "primary",
justified = TRUE,
individual = TRUE,
choiceNames = list("Salt", "PEG-6000"),
choiceValues = list("salt", "peg6000"),
selected = "salt",
checkIcon = list(yes = icon("ok", lib = "glyphicon"))
),
numericInput("vol", label = p("Volume (\\(litres\\))"), value = 1.0, min = 0),
numericInput("pres", label = p("Pressure (\\(MPa\\))"), value = -0.05, max = 0),
numericInput("temp", label = p("Temperature (\\(^{o}C\\))"), value = 25.0),
),
conditionalPanel(
condition = "input.tool_osmp == 'salt'",
column(width = 6,
numericInput("psm", label = p("Molecular weight"), value = 58.4428, min = 0)
),
column(width = 6,
numericInput("dis", label = p("Salt dissociation constant"), value = 1.8, min = 0)
)
),
)
)
)
)
)
)
)
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# -------------------------------------------------------------------------
# GerminaR-----------------------------------------------------------------
# -------------------------------------------------------------------------
#> open https://flavjack.github.io/GerminaR/
#> open https://flavjack.shinyapps.io/germinaquant/
#> author .: Flavio Lozano-Isla (lozanoisla.com)
#> date .: 2021-10-10
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
# packages ----------------------------------------------------------------
# -------------------------------------------------------------------------
#> devtools::install_github("flavjack/GerminaR")
source("msgs.R")
suppressPackageStartupMessages({source("pkgs.R")})
# app ---------------------------------------------------------------------
# -------------------------------------------------------------------------
shinyUI(dashboardPage(skin = "green",
dashboardHeader(title = "GerminaQuant • app",
tags$li(class="dropdown", tags$a(href="https://github.com/sponsors/flavjack", icon("heart"), target="_blank")),
tags$li(class="dropdown", tags$a(href="https://germinar.inkaverse.com/news/" , paste("GerminaR", packageVersion('GerminaR')), target="_blank"))
),
# Sider -------------------------------------------------------------------
dashboardSidebar(
sidebarMenu(
menuItem("Presentacion", tabName = "intro", icon = icon("home")),
menuItem("Fieldbook", tabName = "fieldbook", icon = icon("file-alt")),
menuItem("Germination", tabName = "germination", icon = icon("seedling")),
menuItem("Exploratory", tabName = "outlier", icon = icon("search")),
menuItem("Statistics", tabName = "stat", icon = icon("chart-pie")),
menuItem("Graphics", tabName = "graph", icon = icon("tint")),
menuItem("InTime", tabName = "germint", icon = icon("hourglass")),
menuItem("Tools", tabName = "tools", icon = icon("wrench"))
)
),
dashboardBody(
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "custom.css")
),
tags$head(includeHTML(("www/analytics.html"))),
tags$head(tags$link(rel="shortcut icon", href="https://flavjack.github.io/GerminaR/reference/figures/logo.png")),
meta() %>%
meta_social(
title = "GerminaR",
description = "Indices and Graphics for Assess Seed Germination Process",
url = "https://flavjack.shinyapps.io/germinaquant/",
image = "https://flavjack.github.io/GerminaR/reference/figures/logo.png",
image_alt = "GerminaR"
),
tabItems(
# presentation ------------------------------------------------------------
# -------------------------------------------------------------------------
tabItem(tabName = "intro",
shiny::fluidRow(
box(
title = "GerminaQuant",
width = 3,
status = "primary",
solidHeader = T,
HTML('
<p>
<strong>GerminaQuant</strong> for R is a web application based in R,
you can use the app in your desktop installing the <em><strong>GerminaR</strong></em> package:
</p>
Install the package in the R console
<br>
<code>install.packages("GerminaR")</code>
<br>
<br>
For use the interactive app
<br>
<code>GerminaR::GerminaQuant()</code>
<br>
<br>
<div id=footer style="width:100%; margin:auto;">
<div style="display:inline-block; width:48%">
<p style="text-align:center">
<a target="_blank" href="https://flavjack.github.io/GerminaR/"><img src="https://pkgdown.r-lib.org/reference/figures/logo.png" style="height:75px" title="GerminaR" alt="GerminaR"></a>
<span style="display:block;"><small>GerminaR</small></span>
</p></div>
<div style="display:inline-block; width:48%">
<p style="text-align:center">
<a target="_blank" href="https://youtube.com/playlist?list=PLSQMdOu57lj9QUoA6JLuv0nBTYacuyrbg"><img src="https://lozanoisla.com/img/youtube.png" style="height:70px" title="Demo" alt="Demo"></a>
<span style="display:block;"><small>Demo</small></span>
</p></div>
</div>
')
),
box(width = 5,
title = "Characteristics",
status = "danger",
solidHeader = T,
p("GerminaQuant for R is based in GerminaR R package, a highly interactive data analysis platform for germination analysis,
tool develpment for the Plant Physiology Laboratory (UFPE).
It is result of a continuous effort to improve data collection, quality, analysis and open access publication.
The recent iteration simultaneously also represents efforts to unify best practices from experiences in germination data management.
One of the main new characteristics of the current software development platform established is the web-based interface
which provides also a highly interactive environment. It could be used both online and offline and on desktop as well as tablets and laptops.
The aime is support the broader research community working on all aspects with germination studies."),
HTML("
<h5><b>Features</b></h5>
<p>
<ol>
<li> Allow calculate the principal germination indices.</li>
<li> Statistical analysis for germination.</li>
<li> Easy way to plot the results.</li>
</ol>
</p>
")
),
box(
title = "Package Info",
width = 4,
status = "success",
solidHeader = T,
p(strong("Publication")),
HTML('<p><strong>Flavio Lozano-Isla</strong>; <strong>Omar E. Benites-Alfaro</strong>, and<strong> Marcelo F. Pompelli</strong>. <strong>2019</strong>.
GerminaR: An R package for germination analysis with the interactive web application “GerminaQuant for R.”
Ecological Research 34(2): 339–346. doi: <a href="http://doi.org/10.1111/1440-1703.1275">doi.org/10.1111/1440-1703.1275</a>.</p>'),
br(),
HTML('
<div id=footer style="width:100%; margin:auto;">
<div style="display:inline-block; width:32%">
<p style="text-align:center">
<a target="_blank" href="https://github.com/Flavjack/GerminaR"><img src="https://github.githubassets.com/images/modules/logos_page/Octocat.png" style="height:80px" title="Github" alt="Github"></a>
<span style="display:block;"><small>Github</small></span>
</p></div>
<div style="display:inline-block; width:32%">
<p style="text-align:center">
<a target="_blank" href="https://CRAN.R-project.org/package=GerminaR"><img src="https://flavjack.github.io/GerminaR/reference/figures/logo.png" style="height:80px" title="R cran" alt="GerminaR"></a>
<span style="display:block;"><small>CRAN</small></span>
</p></div>
<div style="display:inline-block; width:32%">
<p style="text-align:center">
<a target="_blank" href="https://flavjack.shinyapps.io/germinaquant/"><img src="https://flavjack.github.io/GerminaR/img/GerminaQuant.png" style="height:80px" title="GerminaQuant" alt="GerminaQuant for R"></a>
<span style="display:block;"><small>GerminaQuant</small></span>
</p></div>
</div>
'),
hr(),
HTML('<p>If you have any question, comment or suggestion you can write at <a href="mailto:flavjack@gmail.com">flozano@lamolina.edu.pe</a></p>')
)
)
),
# fieldbook -------------------------------------------------------------
tabItem(tabName = "fieldbook",
box(
status = "info",
width = 12,
background = "black"
, height = "120px",
column(width = 6,
h4(icon("google"), "Google SpreadSheet (URL)", width = "100%"),
textInput("import_gsheet",
label = NULL ,
width = "100%",
value = "https://docs.google.com/spreadsheets/d/1QziIXGOwb8cl3GaARJq6Ez6aU7vND_UHKJnFcAKx0VI/edit#gid=137089581")
),
column(width = 4,
h4(icon("file-excel"), "Excel file (.xlsx)", width = "100%"),
fileInput('import_excel'
, multiple = FALSE
, label = NULL
, accept = c(".xlsx")
)
),
column(width = 1,
h4("Sheet", width = "100%"),
numericInput("sheetdt", label = NULL, value = 1, step = 1, min = 1)
),
column(width = 1,
h4( "Update", width = "100%"),
actionButton(inputId = "reload", label = "", icon("sync"), width = "100%")
)
),
shiny::fluidRow(
box(
status = "danger",
solidHeader = T,
width = 10,
htmlOutput("data_viewer")
),
# Germination parameters --------------------------------------------------
box(
status = "danger",
solidHeader = T,
width = 2,
title = 'Parameters',
textInput("SeedN", label = strong("Seeds (column name)"), value = "seeds"),
textInput("evalName", label = strong("Evaluations (prefix)"), value = "D")
)
)
),
# Germination analisys ----------------------------------------------------
tabItem(tabName = "germination",
shiny::fluidRow(
box(width = 12,
DT::dataTableOutput("summary"),
br(),
actionButton(inputId= 'indicesLink', label = "Indices info"
, icon = icon("seedling")
, onclick ="window.open('https://germinar.inkaverse.com/articles/introduction.html', '_blank')"
)
)
)
),
# outliers ----------------------------------------------------------------
tabItem(tabName = "outlier",
box(width = 6, background = "black",
column(width = 4,
uiOutput("bpy")
),
column(width = 4,
uiOutput("bpx")
),
column(width = 4,
uiOutput("bpz")
),
column(width = 4,
textInput(inputId ="bply", label = "Y label", value = "")
),
column(width = 4,
textInput(inputId ="bplx", label = "X label", value = "")
),
column(width = 4,
textInput(
inputId ="bplz",
label = "Legend label",
value = "")
)
),
box(width = 3, background = "black",
column(width = 6,
textInput(
inputId ="bpbrk"
, label = "Y limits"
, value = NULL
, placeholder = "0*100*20"
)
),
column(width = 6,
textInput(
inputId ="bprot"
, label = "X rotation"
, value = "0*0.5*0.5"
, placeholder = "angle*h*v"
)
),
column(width = 12,
textInput(
inputId ="bpopt"
, label = "Opt"
, placeholder = "extra layer"
)
)
),
box(width = 3, background = "black",
column(width = 6,
numericInput(
inputId ="bpwd"
, label = "Width (cm)"
, value = 20
, step = 2
)
),
column(width = 6,
numericInput(
inputId = "bphg"
, label = "Height (cm)"
, value = 10
, step = 2
)
),
column(width = 6,
numericInput(
inputId ="bprs"
, label = "Resolution (dpi)"
, value = 100
, step = 50
)
),
column(width = 6,
selectInput(
inputId = "bplg"
, label = "Legend"
, choices = c("top", "bottom", "left", "right", "none")
)
),
),
shiny::fluidRow(
box(width = 12,
div(imageOutput("boxplot"), align = "center")
)
)
),
# statistics -------------------------------------------------------------
tabItem(tabName = "stat",
shiny::fluidRow(
box(width = 5, background = "black",
column(width = 5,
radioButtons(inputId = "stat_model"
, label = "Model parameters"
, choices = c("auto", "manual")
, inline = TRUE
)
),
column(width = 7,
br(),
verbatimTextOutput("model_formula")
),
column(width = 12,
uiOutput("stat_response")
),
hr(),
conditionalPanel(
condition = "input.stat_model == 'auto'",
column(width = 8,
uiOutput("stat_factor")
),
column(width = 4,
uiOutput("stat_block")
),
),
conditionalPanel(
condition = "input.stat_model == 'manual'",
column(width = 12,
textInput(inputId = "stat_model_factors"
, label = "Experiment model factors"
, placeholder = "e.g. block + factor1*factor2"
)
),
),
column(width = 6,
uiOutput("stat_comparison")
),
column(width = 3,
numericInput("stsig",
label = "Significance",
value = 0.05,
min = 0,
max = 5,
step = 0.01)
),
column(width = 3,
selectInput("stmc",
label = "Type",
choices = c("tukey", "duncan", "snk"),
selected = "snk")
),
column(width = 12,
verbatimTextOutput("tbav")
),
column(width = 12,
DT::dataTableOutput("stat_summary")
)
),
box(width = 7,
box(title = "Summary table",
solidHeader = T,
width = 12,
collapsible = T,
collapsed = T,
status = "primary",
DT::dataTableOutput("mnc")
),
box(title = "Model diagnostic",
solidHeader = T,
width = 12,
collapsible = T,
collapsed = T,
status = "danger",
plotOutput("modelplots")
)
)
)
),
# graphics ----------------------------------------------------------------
# -------------------------------------------------------------------------
tabItem(tabName = "graph",
fluidRow(
column( width = 12,
box(width = 6, title = NULL, background = "blue",
column(width = 4,
textInput(
inputId ="plot_ylab",
label = "Y label")
),
column(width = 4,
textInput(inputId ="plot_xlab", label = "X label")
),
column(width = 4,
textInput(inputId ="plot_glab"
, label = "Group label")
),
column(width = 4,
HTML("<b>Model</b>"),
br(),
br(),
textOutput("graph_formula")
),
column(width = 4,
textInput(inputId ="plot_xbrakes"
, label = "X brake labels (,)")
),
column(width = 4,
textInput(inputId ="plot_gbrakes"
, label = "Group brake labels (,)")
),
),
box(width = 3, background = "black",
column(width = 6,
textInput(
inputId ="plot_ylimits"
, label = "Y limits"
, value = NULL
, placeholder = "0*100*20"
)
),
column(width = 6,
textInput(
inputId ="plot_xrotation"
, label = "X rotation"
, value = "0*0.5*0.5"
, placeholder = "angle*h*v"
)
),
column(width = 12,
textInput(
inputId ="plot_opt"
, label = "Opt"
, placeholder = "extra layer"
)
)
),
box(width = 3, background = "black",
column(width = 6,
numericInput(
inputId ="plot_width"
, label = "Width (cm)"
, value = 20
, step = 2
)
),
column(width = 6,
numericInput(
inputId = "plot_height"
, label = "Height (cm)"
, value = 10
, step = 2
)
),
column(width = 6,
numericInput(
inputId ="plot_res"
, label = "Resolution (dpi)"
, value = 100
, step = 50
)
),
column(width = 6,
selectInput(
inputId = "plot_legend"
, label = "Legend"
, choices = c("top"
, "bottom"
, "left"
, "right"
, "none")
)
),
),
shiny::fluidRow(
box(width = 10,
div(imageOutput("plotgr"), align = "center")
),
column(width = 2,
column(width = 12,
radioButtons(
inputId ="plot_type",
label = "Type",
choices = c("bar", "line"),
inline = TRUE
)
),
column(width = 12,
radioButtons(
inputId ="plot_color",
label = "Color",
choices = c("yes"
, "no" = "none"
),
inline = TRUE)
),
column(width = 12,
radioButtons(
inputId ="plot_sig",
label = "Significance",
choices = c("yes" = "sig"
, "no" = "none"
),
inline = TRUE)
),
column(width = 12,
radioButtons(
inputId ="plot_error",
label = "Error",
choices = c("ste"
, "std"
, "no" = "none"
),
inline = TRUE)
)
)
)
)
)
),
# Germination in time -----------------------------------------------------
# -------------------------------------------------------------------------
tabItem(tabName = "germint",
fluidRow(
column( width = 12,
box(width = 6, title = NULL, background = "blue",
column(width = 4,
textInput(
inputId ="intime_ylab",
label = "Y label"
, value = "Germination ('%')")
),
column(width = 4,
textInput(inputId ="intime_xlab"
, label = "X label"
, value = "Time")
),
column(width = 4,
textInput(inputId ="intime_glab"
, label = "Group label")
),
column(width = 4,
uiOutput('smvar')
),
column(width = 4,
# textInput(inputId ="intime_xbrakes"
# , label = "X brake labels (,)"
# )
),
column(width = 4,
textInput(inputId ="intime_gbrakes"
, label = "Group brake labels (,)")
),
),
box(width = 3, background = "black",
column(width = 6,
textInput(
inputId ="intime_ylimits"
, label = "Y limits"
, value = NULL
, placeholder = "0*100*20"
)
),
column(width = 6,
textInput(
inputId ="intime_xrotation"
, label = "X rotation"
, value = "0*0.5*0.5"
, placeholder = "angle*h*v"
)
),
column(width = 12,
textInput(
inputId ="intime_opt"
, label = "Opt"
, placeholder = "extra layer"
)
)
),
box(width = 3, background = "black",
column(width = 6,
numericInput(
inputId ="intime_width"
, label = "Width (cm)"
, value = 20
, step = 2
)
),
column(width = 6,
numericInput(
inputId = "intime_height"
, label = "Height (cm)"
, value = 10
, step = 2
)
),
column(width = 6,
numericInput(
inputId ="intime_res"
, label = "Resolution (dpi)"
, value = 100
, step = 50
)
),
column(width = 6,
selectInput(
inputId = "intime_legend"
, label = "Legend"
, choices = c("top"
, "bottom"
, "left"
, "right"
, "none")
)
),
),
shiny::fluidRow(
box(width = 10,
div(imageOutput("intime_plot"), align = "center")
),
column(width = 2,
column(width = 12,
radioButtons(
inputId ="intime_type",
label = "Type",
choices = c("percentage", "relative"),
selected = "percentage",
inline = F)
),
column(width = 12,
radioButtons(
inputId ="intime_color",
label = "Color",
choices = c("yes"
, "no" = "none"
),
inline = TRUE)
),
column(width = 12,
radioButtons(
inputId ="intime_error",
label = "Error",
choices = c("ste"
, "std"
, "no" = "none"
),
inline = TRUE)
)
)
)
)
)
),
# tools -------------------------------------------------------------------
tabItem(tabName = "tools", withMathJax(),
shiny::fluidRow(
box(width = 7,
title = "Osmotic potencial",
status = "primary",
solidHeader = T,
br(),
p("The osmotic potencial, can be measured directly with an osmometer, or it can be calculated from the solute concentration."),
hr(),
p("For a salt, you can use the van't Hoff relation: $$\\psi_s = -RTC_i$$ where: \\(R\\) is the gas constant (i.e. \\(0.0083 L/atm/mol/K\\)), \\(T\\) is the absolute temperature in degrees in Kelvin (\\(273.15^{o}C\\)),
\\(C\\) is the solute concentration in \\(mol*L^{-1}\\), and \\(i\\) is the dissociation constant of the salt. (i.e. \\(NaCl = 1.8, KCl = 1.8, CaCl_2 = 2.4, sacarose = 1\\)). The unit for \\(\\psi_s\\) is \\(MPa\\)"),
hr(),
p("For", em("PEG-6000"), "the osmotic potentials can be calculated as described by", a("Michel and Kaufmann (1973):", href = "http://www.plantphysiol.org/content/51/5/914.abstract", target="_blank"), "$$\\psi_s = -(1.18*10^{-2})C - (1.18*10^{-4})C^2 + (2.67*10^{-4})CT + (8.39*10^{-7})C^2T$$
where: \\(C\\) is the concentration of", em("PEG-6000"), "in \\(g*L^{-1}\\) and \\(T\\) is the temperature in degrees \\(^{o}C\\). The unit for \\(\\psi_s\\) is \\(bar (0.1 MPa)\\)."),
br()
),
box(
title = "Calculator",
status = "info",
solidHeader = T,
width = 5,
column(width = 12,
h2(textOutput("ops")),
tags$style(type="text/css", "#ops { height: 50px; width: 100%; text-align:center; font-size: 35px;}")
),
column(width = 12,
radioGroupButtons(
inputId = "tool_osmp",
status = "primary",
justified = TRUE,
individual = TRUE,
choiceNames = list("Salt", "PEG-6000"),
choiceValues = list("salt", "peg6000"),
selected = "salt",
checkIcon = list(yes = icon("ok", lib = "glyphicon"))
),
numericInput("vol", label = p("Volume (\\(litres\\))"), value = 1.0, min = 0),
numericInput("pres", label = p("Pressure (\\(MPa\\))"), value = -0.05, max = 0),
numericInput("temp", label = p("Temperature (\\(^{o}C\\))"), value = 25.0),
),
conditionalPanel(
condition = "input.tool_osmp == 'salt'",
column(width = 6,
numericInput("psm", label = p("Molecular weight"), value = 58.4428, min = 0)
),
column(width = 6,
numericInput("dis", label = p("Salt dissociation constant"), value = 1.8, min = 0)
)
),
)
)
)
)
)
)
)
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