inst/DRomicsInterpreter-shiny/ui.R
In aursiber/DRomics: Dose Response for Omics
## JavaScript that dis/enables the ABILITY to click the tab (without changing aesthetics)
# app_jscode <-
# "shinyjs.disableTab = function(name) {
# var tab = $('.nav li a[data-value=' + name + ']');
# tab.bind('click.tab', function(e) {
# e.preventDefault();
# return false;
# });
# tab.addClass('disabled');
# }
# shinyjs.enableTab = function(name) {
# var tab = $('.nav li a[data-value=' + name + ']');
# tab.unbind('click.tab');
# tab.removeClass('disabled');
# }"
## css snipit that makes it LOOK like we are/n't able click the tab (with outchanging functionality)
app_css <-
".nav li a.disabled {
background-color: #aaa !important;
color: #333 !important;
cursor: not-allowed !important;
border-color: #aaa !important;
}
.progress-bar {
background-color: #9c5c16;
}
.js-irs-0 .irs-single, .js-irs-0 .irs-bar-edge, .js-irs-0 .irs-bar {
background: #9c5c16;
border-top: 1px #9c5c16 ;
border-bottom: 1px #9c5c16 ;
}
label > input[type='radio'] + *::before {
content: '';
margin: 4px 0 0;
width: 13px;
height: 13px;
position: absolute;
margin-left: -20px;
border-radius: 50%;
border-style: solid;
border-width: 0.1rem;
border-color: #9c5c16;
}
label > input[type='radio']:checked + *::before {
background: radial-gradient(white 0%, white 30%, #9c5c16 30%, #9c5c16);
border-color: #9c5c16;
}
label > input[type='checkbox'] {
opacity: 0;
position: absolute;
}
label > input[type='checkbox'] + *::before {
content: '';
position: absolute;
margin: 4px 0 0;
margin-left: -20px;
align: center;
width: 13px;
height: 13px;
margin-right: 1rem;
border-radius: 0%;
border-style: solid;
border-width: 0.1rem;
border-color: #9c5c16;
}
label > input[type='checkbox']:checked + *::before {
content: '';
width: 13px;
height: 13px;
background-color: #9c5c16;
}
"
ui <- fluidPage(
shinyjs::useShinyjs(),
# shinyjs::extendShinyjs(text = app_jscode, functions = c('disableTab','enableTab')),
shinyjs::inlineCSS(app_css),
titlePanel(
tags$head(tags$link(rel = "icon", type = "image/png", href = "logodromics-dr.png"), tags$title(" DRomicsInterpreter-shiny"))
),
br(),
navbarPage(title = "",
tabPanel(img(src = "logodromics.png", width = 180),
fluidRow(
br(), br(),
HTML("<center><font face=verdana size=6 color=#9c5c16>Welcome to the DRomicsInterpreter-shiny application</font></center>"),
HTML("<center><font face=verdana size=5 color=#9c5c16>A second workflow for interpretation in light of a biological annotation</font></center>"),
br(), br(),
fixedRow(
column(5, offset = 1,
br(),
p(strong("Links and resources")),
p("The DRomicsInterpreter-shiny application runs on the ",
a("shiny server of the LBBE", href = "http://lbbe-shiny.univ-lyon1.fr/", TARGET="_blank", style="color:#f28d0f;"),
"with the develoment version of the DRomics package (available on ",
a("Github", href = "https://github.com/aursiber/DRomics", TARGET="_blank", style="color:#f28d0f;"),
"). DRomics is also an R package, available on ",
a("CRAN", href = "https://cran.r-project.org/package=DRomics", TARGET="_blank", style="color:#f28d0f;"), ".",
" You can find more information and help about the DRomicsInterpreter-shiny application and the DRomics package on ",
a("this web page", href = "https://lbbe.univ-lyon1.fr/fr/dromics", TARGET="_blank", style="color:#f28d0f;"),
". Reading the vignette first and using the cheat sheet (both are available on this ",
a("this page", href = "https://lbbe.univ-lyon1.fr/fr/dromics", TARGET="_blank", style="color:#f28d0f;"),
") are recommended. "),
p(helpText("If there seems to be a problem with the application, please send an explanatory e-mail at aurelie.siberchicot - at - univ-lyon1.fr.")),
br(),
p(strong("Contact")),
p("If you have any need that is not yet covered, any feedback on the package / Shiny app, or any training needs, feel free to email us at ", strong("dromics@univ-lyon1.fr"), "."),
p("Issues can be reported on",
a("https://github.com/aursiber/DRomics/issues", href = "https://github.com/aursiber/DRomics/issues", TARGET = "_blank", style="color:#f28d0f;"), ".")
),
column(5,
br(),
p(strong("Citation and publications")),
p("If you use Dromics Shiny App, you should cite:"),
p(em("DRomics, a workflow to exploit dose-response omics data in ecotoxicology."),
"Delignette-Muller ML, Siberchicot A, Larras F, Billoir E (2023).",
"Peer Community Journal.",
a("https://peercommunityjournal.org/articles/10.24072/pcjournal.325/", title = "https://peercommunityjournal.org/articles/10.24072/pcjournal.325/", href = "https://peercommunityjournal.org/articles/10.24072/pcjournal.325/", TARGET = "_blank", style="color:#9c5c16;")),
p(em("DRomics: a turnkey tool to support the use of the dose-response framework for omics data in ecological risk assessment."),
"Larras F, Billoir E, Baillard V, Siberchicot A, Scholz S, Wubet T, Tarkka M, Schmitt-Jansen M and Delignette-Muller ML (2018).",
"Environmental Science & Technology.",
a("https://doi.org/10.1021/acs.est.8b04752", title = "https://doi.org/10.1021/acs.est.8b04752", href = "https://pubs.acs.org/doi/10.1021/acs.est.8b04752", TARGET = "_blank", style="color:#9c5c16;"),
" (freely available at: ",
a("https://hal.science/hal-02309919", title = "https://hal.science/hal-02309919", href = "https://hal.science/hal-02309919", TARGET = "_blank", style="color:#9c5c16;"), ")."),
br(),
p("You can also look at the following citation for a complete example of use:"),
p(em("A multi-omics concentration-response framework uncovers novel understanding of triclosan effects in the chlorophyte Scenedesmus vacuolatus."),
"Larras F, Billoir E, Scholz S, Tarkka M, Wubet T, Delignette-Muller ML, Schmitt-Jansen M (2020). Journal of Hazardous Materials.",
a("https://doi.org/10.1016/j.jhazmat.2020.122727", href = "https://doi.org/10.1016/j.jhazmat.2020.122727", TARGET = "_blank", style="color:#f28d0f;"))
)),
hr(style='width: 80%;'),
br(),
fluidRow(column(10, offset = 1, align ="center",
div(style="display: inline-block; width: 30%;", a(img(src = "https://lbbe.univ-lyon1.fr/sites/default/files/icons/logo_1.svg"), href="https://lbbe.univ-lyon1.fr/", TARGET="_blank")),
div(style="display: inline-block; width: 15%;", a(img(src = "logoVetAgroSup.jpg", height = 100), href="http://www.vetagro-sup.fr/", TARGET="_blank")),
div(style="display: inline-block; width: 30%;", a(img(src = "logoLyon1.png", height = 80), href="https://www.univ-lyon1.fr/", TARGET="_blank")),
div(style="display: inline-block; width: 20%;", a(img(src = "LogoUniversiteLorraine.png", height = 80), href="http://www.univ-lorraine.fr/", TARGET="_blank"))
))
)
),
####################################################################################
####### STEP 1 #####################################################################
####################################################################################
tabPanel(HTML("<font face=verdana size=3 color=#9c5c16>Step 1</font>"),
br(), HTML("<font face=verdana size=5 color=#9c5c16><b>Import and merge of DRomics results and annotation data</b></font>"), br(), br(), br(),
fluidRow(
column(1,
numericInput("nbLevel", "Number of experimental levels", value = 1, min = 1, max = 10, step = 1)
),
column(2, style = "margin-top: 25px;padding:20px;",
shinyBS::bsButton("nblevel_help", label = "", icon = icon("info"), size = "small"),
shinyBS::bsPopover("nblevel_help", "", texthelpnblevel, placement = "right", trigger = "hover", options = NULL)
),
column(2,
textInput("maxDoseXScale", "Maximal dose/concentration for definition of x-scale of plots", width = "100%")
),
column(2, style = "margin-top: 25px;padding:20px;",
shinyBS::bsButton("maxdosexscale_help", label = "", icon = icon("info"), size = "small"),
shinyBS::bsPopover("maxdosexscale_help", "", texthelpmaxdosexscale, placement = "right", trigger = "hover", options = NULL)
),
column(4, style = "border-style: solid; border-color: #9c5c16; padding:10px",
"Find here files for two examples (a file containing the DRomics results and another file containing biological annotations):",
h5("- an example about contigs: the ", a("Dromics output", href = "DRomicspkg/triclosanSVcontigres.txt", TARGET = "_blank", style="text-decoration:underline; color:#9c5c16;", download = 'triclosanSVcontigres.txt'),
"and the ", a("annotation data", href = "DRomicspkg/triclosanSVcontigannot.txt", TARGET = "_blank", style="text-decoration:underline; color:#9c5c16;", download = 'triclosanSVcontigannot.txt')),
h5("- an example about metabolites: the ", a("DRomics output", href = "DRomicspkg/triclosanSVmetabres.txt", TARGET = "_blank", style="text-decoration:underline; color:#9c5c16;", download = 'triclosanSVmetabres.txt'),
"and the ", a("annotation data", href = "DRomicspkg/triclosanSVmetabannot.txt", TARGET = "_blank", style="text-decoration:underline; color:#9c5c16;", download = 'triclosanSVmetabannot.txt')),
)
),
br(),
uiOutput("inputstep1"),
fixedRow(
div(align = "center", actionButton("buttonRunStep1", "Merge and Combine", icon = icon("object-group"), style='font-size:150%; color:#111111; background-color:#f28d0f')), br(), br(),
conditionalPanel(
condition = "input.nbLevel > 1",
span(textOutput("txtcolumnidannot"), style = 'color:#9c5c16;font-size:large;'), br(), br()
),
shinyjs::hidden(div(id = 'text1_step1',
style = 'color:#9c5c16; font-size:large;line-height: 50px;',
"Structure of the data frame merged and combined")),
verbatimTextOutput("strmergeddata"), br(), br(),
shinyjs::hidden(div(id = 'text2_step1',
style = 'color:#9c5c16; font-size:large;line-height: 50px;',
"First 3 lines of each experimental level in the data frame merged and combined")),
uiOutput("headmergeddata"),
br(), br()
)
),
####################################################################################
####### STEP 2 #####################################################################
####################################################################################
tabPanel(HTML("<font face=verdana size=3 color=#9c5c16>Step 2</font>"),
value = "step2",
br(), HTML("<font face=verdana size=5 color=#9c5c16><b>Trend and sensitivity plots</b></font>"), br(), br(), br(),
wellPanel(
fixedRow(
column(3, style='border-right:1px solid #9c5c16;',
HTML("<font face=verdana size=3 color=#9c5c16><b>Selection of annotation groups to plot </b></font>"),
shinyBS::bsButton("helplabel1step2", label = "", icon = icon("info"), size = "small", style="color:#9c5c16"),
shinyBS::bsPopover("helplabel1step2", "", helplabel1step2, placement = "right", trigger = "hover", options = list(container = "body")),
br(),
br(),
fluidRow(
conditionalPanel(
condition = "input.nbLevel > 1",
column(6,
checkboxInput("keepAllExplev", label = HTML("<b>Keep all experimental levels</b>"), value = FALSE)
),
column(1, style = "margin-top: 5px",
shinyBS::bsButton("helplabel2step2", label = "", icon = icon("info"), size = "small", style="color:#9c5c16"),
shinyBS::bsPopover("helplabel2step2", "", helplabel2step2, placement = "right", trigger = "hover", options = list(container = "body"))
)
)
),
br(),
sliderInput("minNbItem", "Minimum for the number of items",
width = "90%",
min = 1, max = 10, step = 1, ticks = TRUE,
value = 3),
numericInput("BMDmax", label = "Maximum for the BMD summary value", value = 0, min = 0, step = 0.1, width = "70%")
),
column(1,
checkboxInput("BMDlogtransfoSensitivityplot", label = HTML("<b>Log transformation of the BMD</b>"), value = TRUE),
),
column(1,
radioButtons("BMDtype", label = "BMD type",
choices = list("zSD" = "zSD",
"xfold" = "xfold")
)
),
column(1,
radioButtons("BMDsummarysensitivityPlot", label = "BMD summary",
choices = list("First quartile" = "first.quartile",
"Median" = "median",
"Median and IQR" = "median.and.IQR")
)),
column(2,
# if several experimental level
conditionalPanel(condition = "input.nbLevel > 1",
radioButtons("ordering_moreonelev", label = "Ordering of the annotations",
choices = list("alphabetic order" = "alphaorder_moreonelev",
"ordered by total number of items in all the experimental levels" = "numbitemorder_moreonelev",
"specific order" = "specificorder_moreonelev"))
),
# if only one experimental level
conditionalPanel(condition = "input.nbLevel == 1",
radioButtons("ordering_onelev", label = "Ordering of the annotations",
choices = list("alphabetic order" = "alphaorder_onelev",
"ordered by number of items" = "numbitemorder_onelev",
"ordered by BMD summary value" = "BMDorder_onelev",
"specific order" = "specificorder_onelev"))
),
),
column(3,
conditionalPanel(condition = "input.ordering_moreonelev == 'specificorder_moreonelev' | input.ordering_onelev == 'specificorder_onelev'",
uiOutput("specificorder", style="font-size:85%;")
)
)
)),
div(align = "center", actionButton("buttonRunStep2", "Run", icon = icon("fas fa-gear"), style='font-size:200%; color:#111111; background-color:#f28d0f')), br(), br(),
### outputs
br(), br(),
conditionalPanel(
condition = "input.buttonRunStep2 != 0",
fluidRow(
column(2, offset = 1, style = 'color:#9c5c16; font-size:large;line-height: 40px;', "Trend plot"),
column(2, downloadButton("buttonDownloadTrendplot", "Download Trend Plot", icon = icon("fas fa-download")))),
br(), plotOutput("trendplot", width = "100%"),
br(), br(), br(),
fluidRow(
column(2, offset = 1, style = 'color:#9c5c16; font-size:large;line-height: 40px;', "Sensitivity plot"),
column(2, downloadButton("buttonDownloadSensitivityplot", "Download Sensitivity Plot", icon = icon("fas fa-download")))),
br(), plotOutput("sensitivityplot", width = "100%"),
br(), br(), br(),
fluidRow(
column(5, offset = 1, style = 'color:#9c5c16; font-size:large;line-height: 40px;', "Structure of the data frame merged and combined"),
column(2, downloadButton('downloadData', 'Download Data'))),
br(), verbatimTextOutput("filteredsorteddata"),
br(), br(), br(), br()
)
),
####################################################################################
####### STEP 3 #####################################################################
####################################################################################
tabPanel(HTML("<font face=verdana size=3 color=#9c5c16>Step 3</font>"),
value = "step3",
br(), HTML("<font face=verdana size=5 color=#9c5c16><b>BMD plots (with and without gradient)</b></font>"), br(), br(), br(),
wellPanel(
fixedRow(
column(12,
checkboxGroupInput("annotcheckboxBMDplot", label = "Choose at least on annotation"),
actionButton("selectallBMDplot", "Select All"),
actionButton("unselectallBMDplot", "Unselect All")
))),
wellPanel(
fixedRow(
column(3,
checkboxInput("addciBMDplot", label = HTML("<b>Add CI</b> (only for the BMD plot without gradient)"), value = FALSE),
checkboxInput("BMDlogtransfoBMDplot", label = HTML("<b>Log transformation of the BMD</b>"), value = FALSE),
checkboxInput("addlabelBMDplot", label = HTML("<b>Add labels</b>"), value = FALSE)
),
column(2,
radioButtons("facetbycolumnsBMDplot", label = "Facet by (for columns)",
choices = list("Annotation" = "annotation",
"Experimental level" = "explevel")
)),
conditionalPanel(condition = "input.nbLevel > 1",
column(2,
radioButtons("facetbyrowsBMDplot", label = "Facet by (for rows)",
choices = list("Annotation" = "annotation",
"Experimental level" = "explevel")
))
),
column(3,
fixedRow(
checkboxInput("shapebyBMDplot", label = HTML("<b>Shape by trend</b>"), value = FALSE),
checkboxInput("colorbyBMDplot", label = HTML("<b>Color by trend</b> (only for the BMD plot without gradient)"), value = FALSE)
)
)
)
),
div(align = "center", actionButton("buttonRunStep3", "Run", icon = icon("fas fa-gear"), style='font-size:200%; color:#111111; background-color:#f28d0f')),
### outputs
br(), br(),
conditionalPanel(
condition = "input.buttonRunStep3 != 0",
fluidRow(
column(2, offset = 1, style = 'color:#9c5c16; font-size:large;line-height: 40px;', "BMD plot"),
column(2, downloadButton("buttonDownloadBMDplot", "Download BMD Plot", icon = icon("fas fa-download")))),
br(), plotOutput("bmdplot", width = "100%"),
br(), br(), br(),
fluidRow(
column(2, offset = 1, style = 'color:#9c5c16; font-size:large;line-height: 40px;', "BMD plot with gradient"),
column(2, downloadButton("buttonDownloadBMDplotwithgradient", "Download Sensitivity Plot", icon = icon("fas fa-download")))),
br(), plotOutput("bmdplotwithgradient", width = "100%"),
br(), br(), br(), br()
)
),
####################################################################################
####### STEP 4 #####################################################################
####################################################################################
tabPanel(HTML("<font face=verdana size=3 color=#9c5c16>Step 4</font>"),
value = "step4",
br(), HTML("<font face=verdana size=5 color=#9c5c16><b>Curves plot</b></font>"), br(), br(), br(),
wellPanel(
fixedRow(
column(12,
checkboxGroupInput("annotcheckboxCurvesplot", label = "Choose at least on annotation"),
actionButton("selectallCurvesplot", "Select All"),
actionButton("unselectallCurvesplot", "Unselect All")
))),
wellPanel(
fixedRow(
column(4,
splitLayout(cellWidths = c("60%", "40%"),
checkboxInput("doselogtransfoCurvesplot", label = HTML("<b>Dose log transformation</b>"), value = FALSE),
shinyBS::bsButton("helplabel1step4", label = "", icon = icon("info"), size = "small", style="color:#9c5c16"),
shinyBS::bsPopover("helplabel1step4", "", helplabel1step4, placement = "right", trigger = "hover", options = list(container = "body"))
),
numericInput("mindoseCurvesplot", label = "Minimal dose for the x range", value = 0, width = "60%")
),
column(2,
radioButtons("facetbycolumnsCurvesplot", label = "Facet by (for columns)",
choices = list("Annotation" = "annotation",
"Experimental level" = "explevel")
)),
conditionalPanel(condition = "input.nbLevel > 1",
column(2,
radioButtons("facetbyrowsCurvesplot", label = "Facet by (for rows)",
choices = list("Annotation" = "annotation",
"Experimental level" = "explevel")
))
),
column(2,
fixedRow(
checkboxInput("colorbyCurvesplot", label = HTML("<b>Color by trend</b>"), value = TRUE),
checkboxInput("addBMDCurvesplot", label = HTML("<b>Add BMD-BMR values</b>"), value = TRUE)
)
)
)
),
div(align = "center", actionButton("buttonRunStep4", "Run", icon = icon("fas fa-gear"), style='font-size:200%; color:#111111; background-color:#f28d0f')),
### outputs
br(), br(),
conditionalPanel(
condition = "input.buttonRunStep4 != 0",
fluidRow(
column(2, offset = 1, style = 'color:#9c5c16; font-size:large;line-height: 40px;', "Curves plot"),
column(2, downloadButton("buttonDownloadCurvesplot", "Download Curves Plot", icon = icon("fas fa-download")))),
br(), plotly::plotlyOutput("curvesplot", width = "100%"),
br(), br(), br(), br()
)
),
####################################################################################
####### STEP 5 #####################################################################
####################################################################################
tabPanel(HTML("<font face=verdana size=3 color=#9c5c16>R code to go further</font>"),
value = "step5",
fixedRow(
column(8,
br(), HTML("<font face=verdana size=5 color=#9c5c16><b>R CODE TO GO FURTHER</b></font>"), br(), br(), br(),
tags$blockquote("To see what more you can do using the R package, we recommend you to consult the vignette and the cheat sheet",
"(links to all resources ", a("here", href = "https://lbbe.univ-lyon1.fr/fr/dromics", TARGET="_blank", style="color:#f28d0f;"),")."),
br(),
downloadButton("buttonDownRCode", "Download R Code", icon = icon("fas fa-download"), style = 'background-color:#e6e6e6; color:#000000; border-color:#9d9d9d;'), br(), br(),
verbatimTextOutput('printRCode'), br(), br()
))
)
),
hr(),
helpText("If there seems to be a problem with the application, please send an explanatory e-mail at aurelie.siberchicot - at - univ-lyon1.fr.")
)
aursiber/DRomics documentation built on Feb. 6, 2024, 4:28 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
## JavaScript that dis/enables the ABILITY to click the tab (without changing aesthetics)
# app_jscode <-
# "shinyjs.disableTab = function(name) {
# var tab = $('.nav li a[data-value=' + name + ']');
# tab.bind('click.tab', function(e) {
# e.preventDefault();
# return false;
# });
# tab.addClass('disabled');
# }
# shinyjs.enableTab = function(name) {
# var tab = $('.nav li a[data-value=' + name + ']');
# tab.unbind('click.tab');
# tab.removeClass('disabled');
# }"
## css snipit that makes it LOOK like we are/n't able click the tab (with outchanging functionality)
app_css <-
".nav li a.disabled {
background-color: #aaa !important;
color: #333 !important;
cursor: not-allowed !important;
border-color: #aaa !important;
}
.progress-bar {
background-color: #9c5c16;
}
.js-irs-0 .irs-single, .js-irs-0 .irs-bar-edge, .js-irs-0 .irs-bar {
background: #9c5c16;
border-top: 1px #9c5c16 ;
border-bottom: 1px #9c5c16 ;
}
label > input[type='radio'] + *::before {
content: '';
margin: 4px 0 0;
width: 13px;
height: 13px;
position: absolute;
margin-left: -20px;
border-radius: 50%;
border-style: solid;
border-width: 0.1rem;
border-color: #9c5c16;
}
label > input[type='radio']:checked + *::before {
background: radial-gradient(white 0%, white 30%, #9c5c16 30%, #9c5c16);
border-color: #9c5c16;
}
label > input[type='checkbox'] {
opacity: 0;
position: absolute;
}
label > input[type='checkbox'] + *::before {
content: '';
position: absolute;
margin: 4px 0 0;
margin-left: -20px;
align: center;
width: 13px;
height: 13px;
margin-right: 1rem;
border-radius: 0%;
border-style: solid;
border-width: 0.1rem;
border-color: #9c5c16;
}
label > input[type='checkbox']:checked + *::before {
content: '';
width: 13px;
height: 13px;
background-color: #9c5c16;
}
"
ui <- fluidPage(
shinyjs::useShinyjs(),
# shinyjs::extendShinyjs(text = app_jscode, functions = c('disableTab','enableTab')),
shinyjs::inlineCSS(app_css),
titlePanel(
tags$head(tags$link(rel = "icon", type = "image/png", href = "logodromics-dr.png"), tags$title(" DRomicsInterpreter-shiny"))
),
br(),
navbarPage(title = "",
tabPanel(img(src = "logodromics.png", width = 180),
fluidRow(
br(), br(),
HTML("<center><font face=verdana size=6 color=#9c5c16>Welcome to the DRomicsInterpreter-shiny application</font></center>"),
HTML("<center><font face=verdana size=5 color=#9c5c16>A second workflow for interpretation in light of a biological annotation</font></center>"),
br(), br(),
fixedRow(
column(5, offset = 1,
br(),
p(strong("Links and resources")),
p("The DRomicsInterpreter-shiny application runs on the ",
a("shiny server of the LBBE", href = "http://lbbe-shiny.univ-lyon1.fr/", TARGET="_blank", style="color:#f28d0f;"),
"with the develoment version of the DRomics package (available on ",
a("Github", href = "https://github.com/aursiber/DRomics", TARGET="_blank", style="color:#f28d0f;"),
"). DRomics is also an R package, available on ",
a("CRAN", href = "https://cran.r-project.org/package=DRomics", TARGET="_blank", style="color:#f28d0f;"), ".",
" You can find more information and help about the DRomicsInterpreter-shiny application and the DRomics package on ",
a("this web page", href = "https://lbbe.univ-lyon1.fr/fr/dromics", TARGET="_blank", style="color:#f28d0f;"),
". Reading the vignette first and using the cheat sheet (both are available on this ",
a("this page", href = "https://lbbe.univ-lyon1.fr/fr/dromics", TARGET="_blank", style="color:#f28d0f;"),
") are recommended. "),
p(helpText("If there seems to be a problem with the application, please send an explanatory e-mail at aurelie.siberchicot - at - univ-lyon1.fr.")),
br(),
p(strong("Contact")),
p("If you have any need that is not yet covered, any feedback on the package / Shiny app, or any training needs, feel free to email us at ", strong("dromics@univ-lyon1.fr"), "."),
p("Issues can be reported on",
a("https://github.com/aursiber/DRomics/issues", href = "https://github.com/aursiber/DRomics/issues", TARGET = "_blank", style="color:#f28d0f;"), ".")
),
column(5,
br(),
p(strong("Citation and publications")),
p("If you use Dromics Shiny App, you should cite:"),
p(em("DRomics, a workflow to exploit dose-response omics data in ecotoxicology."),
"Delignette-Muller ML, Siberchicot A, Larras F, Billoir E (2023).",
"Peer Community Journal.",
a("https://peercommunityjournal.org/articles/10.24072/pcjournal.325/", title = "https://peercommunityjournal.org/articles/10.24072/pcjournal.325/", href = "https://peercommunityjournal.org/articles/10.24072/pcjournal.325/", TARGET = "_blank", style="color:#9c5c16;")),
p(em("DRomics: a turnkey tool to support the use of the dose-response framework for omics data in ecological risk assessment."),
"Larras F, Billoir E, Baillard V, Siberchicot A, Scholz S, Wubet T, Tarkka M, Schmitt-Jansen M and Delignette-Muller ML (2018).",
"Environmental Science & Technology.",
a("https://doi.org/10.1021/acs.est.8b04752", title = "https://doi.org/10.1021/acs.est.8b04752", href = "https://pubs.acs.org/doi/10.1021/acs.est.8b04752", TARGET = "_blank", style="color:#9c5c16;"),
" (freely available at: ",
a("https://hal.science/hal-02309919", title = "https://hal.science/hal-02309919", href = "https://hal.science/hal-02309919", TARGET = "_blank", style="color:#9c5c16;"), ")."),
br(),
p("You can also look at the following citation for a complete example of use:"),
p(em("A multi-omics concentration-response framework uncovers novel understanding of triclosan effects in the chlorophyte Scenedesmus vacuolatus."),
"Larras F, Billoir E, Scholz S, Tarkka M, Wubet T, Delignette-Muller ML, Schmitt-Jansen M (2020). Journal of Hazardous Materials.",
a("https://doi.org/10.1016/j.jhazmat.2020.122727", href = "https://doi.org/10.1016/j.jhazmat.2020.122727", TARGET = "_blank", style="color:#f28d0f;"))
)),
hr(style='width: 80%;'),
br(),
fluidRow(column(10, offset = 1, align ="center",
div(style="display: inline-block; width: 30%;", a(img(src = "https://lbbe.univ-lyon1.fr/sites/default/files/icons/logo_1.svg"), href="https://lbbe.univ-lyon1.fr/", TARGET="_blank")),
div(style="display: inline-block; width: 15%;", a(img(src = "logoVetAgroSup.jpg", height = 100), href="http://www.vetagro-sup.fr/", TARGET="_blank")),
div(style="display: inline-block; width: 30%;", a(img(src = "logoLyon1.png", height = 80), href="https://www.univ-lyon1.fr/", TARGET="_blank")),
div(style="display: inline-block; width: 20%;", a(img(src = "LogoUniversiteLorraine.png", height = 80), href="http://www.univ-lorraine.fr/", TARGET="_blank"))
))
)
),
####################################################################################
####### STEP 1 #####################################################################
####################################################################################
tabPanel(HTML("<font face=verdana size=3 color=#9c5c16>Step 1</font>"),
br(), HTML("<font face=verdana size=5 color=#9c5c16><b>Import and merge of DRomics results and annotation data</b></font>"), br(), br(), br(),
fluidRow(
column(1,
numericInput("nbLevel", "Number of experimental levels", value = 1, min = 1, max = 10, step = 1)
),
column(2, style = "margin-top: 25px;padding:20px;",
shinyBS::bsButton("nblevel_help", label = "", icon = icon("info"), size = "small"),
shinyBS::bsPopover("nblevel_help", "", texthelpnblevel, placement = "right", trigger = "hover", options = NULL)
),
column(2,
textInput("maxDoseXScale", "Maximal dose/concentration for definition of x-scale of plots", width = "100%")
),
column(2, style = "margin-top: 25px;padding:20px;",
shinyBS::bsButton("maxdosexscale_help", label = "", icon = icon("info"), size = "small"),
shinyBS::bsPopover("maxdosexscale_help", "", texthelpmaxdosexscale, placement = "right", trigger = "hover", options = NULL)
),
column(4, style = "border-style: solid; border-color: #9c5c16; padding:10px",
"Find here files for two examples (a file containing the DRomics results and another file containing biological annotations):",
h5("- an example about contigs: the ", a("Dromics output", href = "DRomicspkg/triclosanSVcontigres.txt", TARGET = "_blank", style="text-decoration:underline; color:#9c5c16;", download = 'triclosanSVcontigres.txt'),
"and the ", a("annotation data", href = "DRomicspkg/triclosanSVcontigannot.txt", TARGET = "_blank", style="text-decoration:underline; color:#9c5c16;", download = 'triclosanSVcontigannot.txt')),
h5("- an example about metabolites: the ", a("DRomics output", href = "DRomicspkg/triclosanSVmetabres.txt", TARGET = "_blank", style="text-decoration:underline; color:#9c5c16;", download = 'triclosanSVmetabres.txt'),
"and the ", a("annotation data", href = "DRomicspkg/triclosanSVmetabannot.txt", TARGET = "_blank", style="text-decoration:underline; color:#9c5c16;", download = 'triclosanSVmetabannot.txt')),
)
),
br(),
uiOutput("inputstep1"),
fixedRow(
div(align = "center", actionButton("buttonRunStep1", "Merge and Combine", icon = icon("object-group"), style='font-size:150%; color:#111111; background-color:#f28d0f')), br(), br(),
conditionalPanel(
condition = "input.nbLevel > 1",
span(textOutput("txtcolumnidannot"), style = 'color:#9c5c16;font-size:large;'), br(), br()
),
shinyjs::hidden(div(id = 'text1_step1',
style = 'color:#9c5c16; font-size:large;line-height: 50px;',
"Structure of the data frame merged and combined")),
verbatimTextOutput("strmergeddata"), br(), br(),
shinyjs::hidden(div(id = 'text2_step1',
style = 'color:#9c5c16; font-size:large;line-height: 50px;',
"First 3 lines of each experimental level in the data frame merged and combined")),
uiOutput("headmergeddata"),
br(), br()
)
),
####################################################################################
####### STEP 2 #####################################################################
####################################################################################
tabPanel(HTML("<font face=verdana size=3 color=#9c5c16>Step 2</font>"),
value = "step2",
br(), HTML("<font face=verdana size=5 color=#9c5c16><b>Trend and sensitivity plots</b></font>"), br(), br(), br(),
wellPanel(
fixedRow(
column(3, style='border-right:1px solid #9c5c16;',
HTML("<font face=verdana size=3 color=#9c5c16><b>Selection of annotation groups to plot </b></font>"),
shinyBS::bsButton("helplabel1step2", label = "", icon = icon("info"), size = "small", style="color:#9c5c16"),
shinyBS::bsPopover("helplabel1step2", "", helplabel1step2, placement = "right", trigger = "hover", options = list(container = "body")),
br(),
br(),
fluidRow(
conditionalPanel(
condition = "input.nbLevel > 1",
column(6,
checkboxInput("keepAllExplev", label = HTML("<b>Keep all experimental levels</b>"), value = FALSE)
),
column(1, style = "margin-top: 5px",
shinyBS::bsButton("helplabel2step2", label = "", icon = icon("info"), size = "small", style="color:#9c5c16"),
shinyBS::bsPopover("helplabel2step2", "", helplabel2step2, placement = "right", trigger = "hover", options = list(container = "body"))
)
)
),
br(),
sliderInput("minNbItem", "Minimum for the number of items",
width = "90%",
min = 1, max = 10, step = 1, ticks = TRUE,
value = 3),
numericInput("BMDmax", label = "Maximum for the BMD summary value", value = 0, min = 0, step = 0.1, width = "70%")
),
column(1,
checkboxInput("BMDlogtransfoSensitivityplot", label = HTML("<b>Log transformation of the BMD</b>"), value = TRUE),
),
column(1,
radioButtons("BMDtype", label = "BMD type",
choices = list("zSD" = "zSD",
"xfold" = "xfold")
)
),
column(1,
radioButtons("BMDsummarysensitivityPlot", label = "BMD summary",
choices = list("First quartile" = "first.quartile",
"Median" = "median",
"Median and IQR" = "median.and.IQR")
)),
column(2,
# if several experimental level
conditionalPanel(condition = "input.nbLevel > 1",
radioButtons("ordering_moreonelev", label = "Ordering of the annotations",
choices = list("alphabetic order" = "alphaorder_moreonelev",
"ordered by total number of items in all the experimental levels" = "numbitemorder_moreonelev",
"specific order" = "specificorder_moreonelev"))
),
# if only one experimental level
conditionalPanel(condition = "input.nbLevel == 1",
radioButtons("ordering_onelev", label = "Ordering of the annotations",
choices = list("alphabetic order" = "alphaorder_onelev",
"ordered by number of items" = "numbitemorder_onelev",
"ordered by BMD summary value" = "BMDorder_onelev",
"specific order" = "specificorder_onelev"))
),
),
column(3,
conditionalPanel(condition = "input.ordering_moreonelev == 'specificorder_moreonelev' | input.ordering_onelev == 'specificorder_onelev'",
uiOutput("specificorder", style="font-size:85%;")
)
)
)),
div(align = "center", actionButton("buttonRunStep2", "Run", icon = icon("fas fa-gear"), style='font-size:200%; color:#111111; background-color:#f28d0f')), br(), br(),
### outputs
br(), br(),
conditionalPanel(
condition = "input.buttonRunStep2 != 0",
fluidRow(
column(2, offset = 1, style = 'color:#9c5c16; font-size:large;line-height: 40px;', "Trend plot"),
column(2, downloadButton("buttonDownloadTrendplot", "Download Trend Plot", icon = icon("fas fa-download")))),
br(), plotOutput("trendplot", width = "100%"),
br(), br(), br(),
fluidRow(
column(2, offset = 1, style = 'color:#9c5c16; font-size:large;line-height: 40px;', "Sensitivity plot"),
column(2, downloadButton("buttonDownloadSensitivityplot", "Download Sensitivity Plot", icon = icon("fas fa-download")))),
br(), plotOutput("sensitivityplot", width = "100%"),
br(), br(), br(),
fluidRow(
column(5, offset = 1, style = 'color:#9c5c16; font-size:large;line-height: 40px;', "Structure of the data frame merged and combined"),
column(2, downloadButton('downloadData', 'Download Data'))),
br(), verbatimTextOutput("filteredsorteddata"),
br(), br(), br(), br()
)
),
####################################################################################
####### STEP 3 #####################################################################
####################################################################################
tabPanel(HTML("<font face=verdana size=3 color=#9c5c16>Step 3</font>"),
value = "step3",
br(), HTML("<font face=verdana size=5 color=#9c5c16><b>BMD plots (with and without gradient)</b></font>"), br(), br(), br(),
wellPanel(
fixedRow(
column(12,
checkboxGroupInput("annotcheckboxBMDplot", label = "Choose at least on annotation"),
actionButton("selectallBMDplot", "Select All"),
actionButton("unselectallBMDplot", "Unselect All")
))),
wellPanel(
fixedRow(
column(3,
checkboxInput("addciBMDplot", label = HTML("<b>Add CI</b> (only for the BMD plot without gradient)"), value = FALSE),
checkboxInput("BMDlogtransfoBMDplot", label = HTML("<b>Log transformation of the BMD</b>"), value = FALSE),
checkboxInput("addlabelBMDplot", label = HTML("<b>Add labels</b>"), value = FALSE)
),
column(2,
radioButtons("facetbycolumnsBMDplot", label = "Facet by (for columns)",
choices = list("Annotation" = "annotation",
"Experimental level" = "explevel")
)),
conditionalPanel(condition = "input.nbLevel > 1",
column(2,
radioButtons("facetbyrowsBMDplot", label = "Facet by (for rows)",
choices = list("Annotation" = "annotation",
"Experimental level" = "explevel")
))
),
column(3,
fixedRow(
checkboxInput("shapebyBMDplot", label = HTML("<b>Shape by trend</b>"), value = FALSE),
checkboxInput("colorbyBMDplot", label = HTML("<b>Color by trend</b> (only for the BMD plot without gradient)"), value = FALSE)
)
)
)
),
div(align = "center", actionButton("buttonRunStep3", "Run", icon = icon("fas fa-gear"), style='font-size:200%; color:#111111; background-color:#f28d0f')),
### outputs
br(), br(),
conditionalPanel(
condition = "input.buttonRunStep3 != 0",
fluidRow(
column(2, offset = 1, style = 'color:#9c5c16; font-size:large;line-height: 40px;', "BMD plot"),
column(2, downloadButton("buttonDownloadBMDplot", "Download BMD Plot", icon = icon("fas fa-download")))),
br(), plotOutput("bmdplot", width = "100%"),
br(), br(), br(),
fluidRow(
column(2, offset = 1, style = 'color:#9c5c16; font-size:large;line-height: 40px;', "BMD plot with gradient"),
column(2, downloadButton("buttonDownloadBMDplotwithgradient", "Download Sensitivity Plot", icon = icon("fas fa-download")))),
br(), plotOutput("bmdplotwithgradient", width = "100%"),
br(), br(), br(), br()
)
),
####################################################################################
####### STEP 4 #####################################################################
####################################################################################
tabPanel(HTML("<font face=verdana size=3 color=#9c5c16>Step 4</font>"),
value = "step4",
br(), HTML("<font face=verdana size=5 color=#9c5c16><b>Curves plot</b></font>"), br(), br(), br(),
wellPanel(
fixedRow(
column(12,
checkboxGroupInput("annotcheckboxCurvesplot", label = "Choose at least on annotation"),
actionButton("selectallCurvesplot", "Select All"),
actionButton("unselectallCurvesplot", "Unselect All")
))),
wellPanel(
fixedRow(
column(4,
splitLayout(cellWidths = c("60%", "40%"),
checkboxInput("doselogtransfoCurvesplot", label = HTML("<b>Dose log transformation</b>"), value = FALSE),
shinyBS::bsButton("helplabel1step4", label = "", icon = icon("info"), size = "small", style="color:#9c5c16"),
shinyBS::bsPopover("helplabel1step4", "", helplabel1step4, placement = "right", trigger = "hover", options = list(container = "body"))
),
numericInput("mindoseCurvesplot", label = "Minimal dose for the x range", value = 0, width = "60%")
),
column(2,
radioButtons("facetbycolumnsCurvesplot", label = "Facet by (for columns)",
choices = list("Annotation" = "annotation",
"Experimental level" = "explevel")
)),
conditionalPanel(condition = "input.nbLevel > 1",
column(2,
radioButtons("facetbyrowsCurvesplot", label = "Facet by (for rows)",
choices = list("Annotation" = "annotation",
"Experimental level" = "explevel")
))
),
column(2,
fixedRow(
checkboxInput("colorbyCurvesplot", label = HTML("<b>Color by trend</b>"), value = TRUE),
checkboxInput("addBMDCurvesplot", label = HTML("<b>Add BMD-BMR values</b>"), value = TRUE)
)
)
)
),
div(align = "center", actionButton("buttonRunStep4", "Run", icon = icon("fas fa-gear"), style='font-size:200%; color:#111111; background-color:#f28d0f')),
### outputs
br(), br(),
conditionalPanel(
condition = "input.buttonRunStep4 != 0",
fluidRow(
column(2, offset = 1, style = 'color:#9c5c16; font-size:large;line-height: 40px;', "Curves plot"),
column(2, downloadButton("buttonDownloadCurvesplot", "Download Curves Plot", icon = icon("fas fa-download")))),
br(), plotly::plotlyOutput("curvesplot", width = "100%"),
br(), br(), br(), br()
)
),
####################################################################################
####### STEP 5 #####################################################################
####################################################################################
tabPanel(HTML("<font face=verdana size=3 color=#9c5c16>R code to go further</font>"),
value = "step5",
fixedRow(
column(8,
br(), HTML("<font face=verdana size=5 color=#9c5c16><b>R CODE TO GO FURTHER</b></font>"), br(), br(), br(),
tags$blockquote("To see what more you can do using the R package, we recommend you to consult the vignette and the cheat sheet",
"(links to all resources ", a("here", href = "https://lbbe.univ-lyon1.fr/fr/dromics", TARGET="_blank", style="color:#f28d0f;"),")."),
br(),
downloadButton("buttonDownRCode", "Download R Code", icon = icon("fas fa-download"), style = 'background-color:#e6e6e6; color:#000000; border-color:#9d9d9d;'), br(), br(),
verbatimTextOutput('printRCode'), br(), br()
))
)
),
hr(),
helpText("If there seems to be a problem with the application, please send an explanatory e-mail at aurelie.siberchicot - at - univ-lyon1.fr.")
)
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