ui.R
In Xinzhu-Fang/shinyNDTr: A web-based interface for neural decoding in R
ui <- dashboardPage(
dashboardHeader(title = "shinyNDTr"),
dashboardSidebar(
sidebarMenu(
# menuItem("Home", tabName = "home"),
menuItem("Binning the raster data", tabName = "bin"),
menuItem("Population Decoding", tabName = "decode")#,
# menuItem("Single Neuron Analysis", tabName = "single")
)),
dashboardBody(
tabItems(
# tabItem(tabName = "home",
# fluidPage(
# shinyFiles::shinyFilesButton("home_loaded_state", lLabels$home_loaded_state, "", multiple = FALSE),
# uiOutput("home_offer_save_state")
# )
# ),
tabItem(tabName = "bin",
navbarPage(title = "",
tabPanel(
title = "Specify binning parameters",
fluidPage(
fluidRow(
column(width = 12,
box(width = NULL,
status = "danger",
solidHeader = TRUE,
title = "Choose a directory of raster data files",
shinyFiles::shinyDirButton("bin_chosen_raster", lLabels$bin_chosen_raster, ""),
helpText("Loaded raster data: "),
textOutput("bin_show_chosen_raster")
),
box(width = 8,
numericInput("bin_bin_width", lLabels$bin_bin_width, value = 10, min = 1),
numericInput("bin_step_size", lLabels$bin_step_size, value = 1, min = 1),
numericInput("bin_start_ind", lLabels$bin_start_ind, value = NULL),
numericInput("bin_end_ind", lLabels$bin_end_ind, value = NULL),
textInput("bin_prefix_of_binned_file_name", lLabels$bin_prefix_of_binned_file_name),
actionButton("bin_bin_data", lLabels$bin_bin_data),
uiOutput("bin_action_error"),
textOutput("bin_show_create_bin_function_run") )
)
)
)
),
tabPanel(
title = "Plot raster data",
fluidPage(
fluidRow(
column(width = 12,
box(
width = NULL,
# shinyFilesButton('files', label='File select', title='Please select a file', multiple=FALSE),
# checkboxInput("bin_bPlot", lLabels$bin_bPlot),
# conditionalPanel(condition = "input.bin_bPlot",
actionButton("bin_pre_neuron", lLabels$bin_pre_neuron),
actionButton("bin_next_neuron", lLabels$bin_next_neuron),
textOutput("bin_show_raster_cur_file_name"),
dataTableOutput('where')
),
tabBox(width = NULL,
title = "",
tabPanel(
title = "Raster plot",
# background = "green",
ribbon = TRUE,
title_side = "top right",
# conditionalPanel(condition = "input.bin_bPlot",
plotOutput("bin_raster_plot")
),
tabPanel(
width = NULL,
title = "PSTH (Peristimulus time histogram)",
# background = "red",
ribbon = TRUE,
title_side = "top right",
# conditionalPanel(condition = "input.bin_bPlot",
plotOutput("bin_PSTH")
)
)
)
)
)
),
tabPanel(
title = "Upload new raster data",
fluidRow(
box(width = NULL,
helpText("We only accept .mat and .Rda format !"),
uiOutput("bin_offer_upload_raster"),
uiOutput("bin_offer_create_raster"),
uiOutput("bin_evil_raster"),
textOutput("bin_show_create_raster_function_run")
)
)
)
)
),
tabItem(tabName = "decode",
navbarPage(title = "",
tabPanel(
title = "Specify decoding papameters",
fluidPage(
fluidRow(
column(width = 12,
tabBox(width = 12,
# tabPanel(
# title = "Upload new binned data",
# width = NULL,
# solidHeader = TRUE, status = "primary",
# uiOutput("DS_offer_upload_bin")
#
# ),
tabPanel(
title = "Data source",
width = NULL,
solidHeader = TRUE,
status = "primary",
box(
width = NULL,
title = "Choose a binned data file",
status = "danger",
solidHeader = TRUE,
shinyFiles::shinyFilesButton("DS_chosen_bin", lLabels$DS_chosen_bin, "", multiple = FALSE),
helpText("Loaded binned data: "),
textOutput("DS_show_chosen_bin")
),
selectInput("DS_type", lLabels$DS_type, c("basic_DS","generalization_DS")),
conditionalPanel(condition = "input.DS_type == 'basic_DS'",
uiOutput("DS_basic_list_of_var_to_decode"),
checkboxInput("DS_bUse_all_levels", "Use all the levels of this variable?", TRUE)
),
conditionalPanel(condition = "!input.DS_bUse_all_levels && input.DS_type == 'basic_DS'",
uiOutput("DS_basic_list_of_levels_to_use")),
conditionalPanel(condition = "input.DS_type == 'generalization_DS'",
uiOutput("DS_gen_list_of_var_to_decode"),
uiOutput("DS_gen_list_of_var_to_use"),
uiOutput("DS_gen_select_num_of_groups"),
uiOutput("DS_gen_list_of_training_level_groups")#,
# uiOutput("DS_gen_list_of_testing_level_groups")
)
),
tabPanel(
title = "Classifier",
width = NULL,
solidHeader = TRUE, status = "primary",
selectInput("CL", "Classifier", all_cl),
box(
width = NULL,
title = "Additional parameters (if applicable)",
conditionalPanel(condition = "input.CL == 'svm_CL'",
selectInput("CL_SVM_kernel",
lLabels$CL_SVM_kernel,
c("linear", "polynomial", "radial", "sigmoid"),
selected = "linear"),
numericInput("CL_SVM_cost",
lLabels$CL_SVM_cost, # of constraints violation / inverse of regularization constant",
1,
min = 0
),
conditionalPanel(condition ="input.CL_SVM_kernel == 'polynomial'",
numericInput("CL_SVM_degree",
lLabels$CL_SVM_degree,
3,
min = 2,
max = 10)),
conditionalPanel(condition = "input.CL_SVM_kernel == 'radial'|input.CL_SVM_kernel == 'polynomial'",
numericInput("CL_SVM_coef0",
lLabels$CL_SVM_coef0, # Constant in the kernel function",
0)),
conditionalPanel(condition = "input.CL_SVM_kernel == 'radial'|input.CL_SVM_kernel == 'polynomial'|input.CL_SVM_kernel == 'sigmoid'",
numericInput("CL_SVM_gamma",
lLabels$CL_SVM_gamma,
NULL)
)
))
),
tabPanel(
title = "Feature preprocessors",
width = NULL,
solidHeader = TRUE, status = "primary",
uiOutput("FP_check_fp"),
uiOutput("FP_select_k_features"),
uiOutput("FP_exclude_k_features")
),
tabPanel(
title = "Cross validator",
width = NULL,
solidHeader = TRUE, status = "primary",
fluidRow(
column(
width = 6,
uiOutput("CV_max_repetition_avail_with_any_site"),
uiOutput("CV_repeat"),
uiOutput("CV_split"),
uiOutput("CV_show_chosen_repetition_info"),
numericInput("CV_resample", lLabels$CV_resample, value = 20, min = 1),
checkboxInput("CV_bDiag", lLabels$CV_bDiag,TRUE)
),
column(
width = 6,
plotlyOutput("CV_show_level_repetition_info")
)
)
),
tabPanel(
title = "Decoder",
width = NULL,
fluidRow(
column(
width = 6,
box(
title = "Create a new script",
width = NULL,
status = "danger",
# background = "red",
solidHeader = TRUE,
radioButtons("DC_script_mode", lLabels$DC_script_mode, c("R", "R Markdown", "MATLAB"), selected = "R"),
uiOutput("DC_offer_scriptize"),
# textinput of filename to be saved if not existing and to be saved as if existing;
uiOutput("DC_offer_save_displayed_script"),
helpText(" or"),
uiOutput("DC_offer_run_decoding")
# )
),
# tabPanel(
# title = "",
# width = NULL,
box(
title = "Load an existing script",
width = NULL,
status = "success",
# background = "aqua",
solidHeader = TRUE,
# script will show upon chosen
shinyFiles::shinyFilesButton("DC_chosenscript_name", lLabels$DC_chosenscript_name, "", multiple = FALSE),
helpText("Displayed script: "),
textOutput("DC_show_chosen_script")
)
),
column(width = 6,
box(width = NULL,
uiOutput("DC_ace")
)
)
)
),
tabPanel(
title = "PDF",
width = NULL,
helpText("Will pop up when done"),
uiOutput("DC_pdf")
)
))
)
)
),
tabPanel(
title = "Plot decoding results",
column(width = 12,
#issue cannot make use of the large blank on the right
box(
title = "Choose the result to plot",
width = NULL,
status = "danger",
solidHeader = TRUE,
shinyFiles::shinyFilesButton("Plot_chosen_result", lLabels$Plot_chosen_result, "", multiple = FALSE),
helpText("Loaded result: "),
textOutput("Plot_show_chosen_result")
),
tabBox(width = NULL,
# title = "Result plot",
tabPanel("Timeseries",
selectInput("Plot_timeseries_result_type", lLabels$Plot_timeseries_result_type,
all_result_type),
plotOutput("Plot_timeseries")
),
tabPanel("TCT heatmap",
selectInput("Plot_tct_result_type", lLabels$Plot_TCT_result_type,
all_result_type),
plotOutput("Plot_tct")
),
tabPanel("PDF of script and result",
actionButton("Plot_create_pdf", lLabels$Plot_create_pdf),
helpText(""),
uiOutput("Plot_pdf")
)
)
)
),
tabPanel(
title = "Upload new binned data",
width = NULL,
box(
title = NULL,
width = NULL,
uiOutput("DS_offer_upload_bin")
)
)
)
)
)
)
)
Xinzhu-Fang/shinyNDTr documentation built on Oct. 11, 2020, 9:03 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
ui <- dashboardPage(
dashboardHeader(title = "shinyNDTr"),
dashboardSidebar(
sidebarMenu(
# menuItem("Home", tabName = "home"),
menuItem("Binning the raster data", tabName = "bin"),
menuItem("Population Decoding", tabName = "decode")#,
# menuItem("Single Neuron Analysis", tabName = "single")
)),
dashboardBody(
tabItems(
# tabItem(tabName = "home",
# fluidPage(
# shinyFiles::shinyFilesButton("home_loaded_state", lLabels$home_loaded_state, "", multiple = FALSE),
# uiOutput("home_offer_save_state")
# )
# ),
tabItem(tabName = "bin",
navbarPage(title = "",
tabPanel(
title = "Specify binning parameters",
fluidPage(
fluidRow(
column(width = 12,
box(width = NULL,
status = "danger",
solidHeader = TRUE,
title = "Choose a directory of raster data files",
shinyFiles::shinyDirButton("bin_chosen_raster", lLabels$bin_chosen_raster, ""),
helpText("Loaded raster data: "),
textOutput("bin_show_chosen_raster")
),
box(width = 8,
numericInput("bin_bin_width", lLabels$bin_bin_width, value = 10, min = 1),
numericInput("bin_step_size", lLabels$bin_step_size, value = 1, min = 1),
numericInput("bin_start_ind", lLabels$bin_start_ind, value = NULL),
numericInput("bin_end_ind", lLabels$bin_end_ind, value = NULL),
textInput("bin_prefix_of_binned_file_name", lLabels$bin_prefix_of_binned_file_name),
actionButton("bin_bin_data", lLabels$bin_bin_data),
uiOutput("bin_action_error"),
textOutput("bin_show_create_bin_function_run") )
)
)
)
),
tabPanel(
title = "Plot raster data",
fluidPage(
fluidRow(
column(width = 12,
box(
width = NULL,
# shinyFilesButton('files', label='File select', title='Please select a file', multiple=FALSE),
# checkboxInput("bin_bPlot", lLabels$bin_bPlot),
# conditionalPanel(condition = "input.bin_bPlot",
actionButton("bin_pre_neuron", lLabels$bin_pre_neuron),
actionButton("bin_next_neuron", lLabels$bin_next_neuron),
textOutput("bin_show_raster_cur_file_name"),
dataTableOutput('where')
),
tabBox(width = NULL,
title = "",
tabPanel(
title = "Raster plot",
# background = "green",
ribbon = TRUE,
title_side = "top right",
# conditionalPanel(condition = "input.bin_bPlot",
plotOutput("bin_raster_plot")
),
tabPanel(
width = NULL,
title = "PSTH (Peristimulus time histogram)",
# background = "red",
ribbon = TRUE,
title_side = "top right",
# conditionalPanel(condition = "input.bin_bPlot",
plotOutput("bin_PSTH")
)
)
)
)
)
),
tabPanel(
title = "Upload new raster data",
fluidRow(
box(width = NULL,
helpText("We only accept .mat and .Rda format !"),
uiOutput("bin_offer_upload_raster"),
uiOutput("bin_offer_create_raster"),
uiOutput("bin_evil_raster"),
textOutput("bin_show_create_raster_function_run")
)
)
)
)
),
tabItem(tabName = "decode",
navbarPage(title = "",
tabPanel(
title = "Specify decoding papameters",
fluidPage(
fluidRow(
column(width = 12,
tabBox(width = 12,
# tabPanel(
# title = "Upload new binned data",
# width = NULL,
# solidHeader = TRUE, status = "primary",
# uiOutput("DS_offer_upload_bin")
#
# ),
tabPanel(
title = "Data source",
width = NULL,
solidHeader = TRUE,
status = "primary",
box(
width = NULL,
title = "Choose a binned data file",
status = "danger",
solidHeader = TRUE,
shinyFiles::shinyFilesButton("DS_chosen_bin", lLabels$DS_chosen_bin, "", multiple = FALSE),
helpText("Loaded binned data: "),
textOutput("DS_show_chosen_bin")
),
selectInput("DS_type", lLabels$DS_type, c("basic_DS","generalization_DS")),
conditionalPanel(condition = "input.DS_type == 'basic_DS'",
uiOutput("DS_basic_list_of_var_to_decode"),
checkboxInput("DS_bUse_all_levels", "Use all the levels of this variable?", TRUE)
),
conditionalPanel(condition = "!input.DS_bUse_all_levels && input.DS_type == 'basic_DS'",
uiOutput("DS_basic_list_of_levels_to_use")),
conditionalPanel(condition = "input.DS_type == 'generalization_DS'",
uiOutput("DS_gen_list_of_var_to_decode"),
uiOutput("DS_gen_list_of_var_to_use"),
uiOutput("DS_gen_select_num_of_groups"),
uiOutput("DS_gen_list_of_training_level_groups")#,
# uiOutput("DS_gen_list_of_testing_level_groups")
)
),
tabPanel(
title = "Classifier",
width = NULL,
solidHeader = TRUE, status = "primary",
selectInput("CL", "Classifier", all_cl),
box(
width = NULL,
title = "Additional parameters (if applicable)",
conditionalPanel(condition = "input.CL == 'svm_CL'",
selectInput("CL_SVM_kernel",
lLabels$CL_SVM_kernel,
c("linear", "polynomial", "radial", "sigmoid"),
selected = "linear"),
numericInput("CL_SVM_cost",
lLabels$CL_SVM_cost, # of constraints violation / inverse of regularization constant",
1,
min = 0
),
conditionalPanel(condition ="input.CL_SVM_kernel == 'polynomial'",
numericInput("CL_SVM_degree",
lLabels$CL_SVM_degree,
3,
min = 2,
max = 10)),
conditionalPanel(condition = "input.CL_SVM_kernel == 'radial'|input.CL_SVM_kernel == 'polynomial'",
numericInput("CL_SVM_coef0",
lLabels$CL_SVM_coef0, # Constant in the kernel function",
0)),
conditionalPanel(condition = "input.CL_SVM_kernel == 'radial'|input.CL_SVM_kernel == 'polynomial'|input.CL_SVM_kernel == 'sigmoid'",
numericInput("CL_SVM_gamma",
lLabels$CL_SVM_gamma,
NULL)
)
))
),
tabPanel(
title = "Feature preprocessors",
width = NULL,
solidHeader = TRUE, status = "primary",
uiOutput("FP_check_fp"),
uiOutput("FP_select_k_features"),
uiOutput("FP_exclude_k_features")
),
tabPanel(
title = "Cross validator",
width = NULL,
solidHeader = TRUE, status = "primary",
fluidRow(
column(
width = 6,
uiOutput("CV_max_repetition_avail_with_any_site"),
uiOutput("CV_repeat"),
uiOutput("CV_split"),
uiOutput("CV_show_chosen_repetition_info"),
numericInput("CV_resample", lLabels$CV_resample, value = 20, min = 1),
checkboxInput("CV_bDiag", lLabels$CV_bDiag,TRUE)
),
column(
width = 6,
plotlyOutput("CV_show_level_repetition_info")
)
)
),
tabPanel(
title = "Decoder",
width = NULL,
fluidRow(
column(
width = 6,
box(
title = "Create a new script",
width = NULL,
status = "danger",
# background = "red",
solidHeader = TRUE,
radioButtons("DC_script_mode", lLabels$DC_script_mode, c("R", "R Markdown", "MATLAB"), selected = "R"),
uiOutput("DC_offer_scriptize"),
# textinput of filename to be saved if not existing and to be saved as if existing;
uiOutput("DC_offer_save_displayed_script"),
helpText(" or"),
uiOutput("DC_offer_run_decoding")
# )
),
# tabPanel(
# title = "",
# width = NULL,
box(
title = "Load an existing script",
width = NULL,
status = "success",
# background = "aqua",
solidHeader = TRUE,
# script will show upon chosen
shinyFiles::shinyFilesButton("DC_chosenscript_name", lLabels$DC_chosenscript_name, "", multiple = FALSE),
helpText("Displayed script: "),
textOutput("DC_show_chosen_script")
)
),
column(width = 6,
box(width = NULL,
uiOutput("DC_ace")
)
)
)
),
tabPanel(
title = "PDF",
width = NULL,
helpText("Will pop up when done"),
uiOutput("DC_pdf")
)
))
)
)
),
tabPanel(
title = "Plot decoding results",
column(width = 12,
#issue cannot make use of the large blank on the right
box(
title = "Choose the result to plot",
width = NULL,
status = "danger",
solidHeader = TRUE,
shinyFiles::shinyFilesButton("Plot_chosen_result", lLabels$Plot_chosen_result, "", multiple = FALSE),
helpText("Loaded result: "),
textOutput("Plot_show_chosen_result")
),
tabBox(width = NULL,
# title = "Result plot",
tabPanel("Timeseries",
selectInput("Plot_timeseries_result_type", lLabels$Plot_timeseries_result_type,
all_result_type),
plotOutput("Plot_timeseries")
),
tabPanel("TCT heatmap",
selectInput("Plot_tct_result_type", lLabels$Plot_TCT_result_type,
all_result_type),
plotOutput("Plot_tct")
),
tabPanel("PDF of script and result",
actionButton("Plot_create_pdf", lLabels$Plot_create_pdf),
helpText(""),
uiOutput("Plot_pdf")
)
)
)
),
tabPanel(
title = "Upload new binned data",
width = NULL,
box(
title = NULL,
width = NULL,
uiOutput("DS_offer_upload_bin")
)
)
)
)
)
)
)
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.
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