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ui.R
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#last_update <- '05-04-2023'
library(shiny)
library(shinyFiles)
library(shinyjs)
library(shinyWidgets)
library(shinyalert)
source("Shiny_Libraries_v1.R")
source("Shiny_Functions_v1.R")
shinyUI(
tagList(
fluidPage(
useShinyjs(),
useShinyalert(),
setBackgroundColor("DarkGray", shinydashboard = TRUE),
setBackgroundColor("LightGray", shinydashboard = FALSE),
titlePanel("Proteome Discoverer Data Processing"),
navlistPanel(widths=c(1,11), id = "nlp1",
tabPanel("Load Page", value = "load", align="center",
br(),
br(),
br(),
br(),
br(),
tags$h1("Loading app...")
),
tabPanel("Load Design", value = "tp_load_design", align="center",
hr(),
tags$h1("Choose and Load the study design file..."),
br(),
shinyFilesButton('design_file', label='Choose Design File', title='Please select excel design file', multiple=FALSE,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
br(),
checkboxInput("primary_group", label = "Use only primary group for filter and impute", value=FALSE),
br(),
actionButton("action_load_design", label = "Load Design File", width = 200,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
br(),
hr(),
br(),
tags$h3("Or load saved dpmsr_set file..."),
shinyFilesButton('dpmsr_set_file', label='Choose dpmsr_set File', title='Choose dpmsr_set File', multiple=FALSE,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
br(),
br(),
actionButton("action_load_dpmsr_set", label = "Load dpmsr_set", width = 200,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
br(),
br(),
hr(),
br(),
tags$h3("If needed clear data and functions..."),
br(),
actionButton("action_clear", label = "Clear Data", width = 200,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
br(),
br(),
br(),
br(),
br(),
br(),
span(textOutput("app_version_text"), style="color:blue; font-size:16px")
), #end tab panel
tabPanel("Load Data", value = "tp_load_data", align="center",
tags$h1("Choose type and load data file"),
hr(),
fluidRow(align = "left",
column(width=3, offset =2,
radioButtons("radio_input", label = h3("Select Input Data Type"),
choices = list("Protein_Peptide" = 1, "Protein" = 2, "Peptide" = 3),
selected = 3)
),
column(width=3, offset =0,
radioButtons("radio_output", label = h3("Select Output Data Type"),
choices = list("Protein" = 1, "Peptide" = 2),
selected = 2)
),
column(width=3, offset =0,
radioButtons("data_source", label = h3("Select Data Source"),
choices = list("Proteome Discoverer" = 1, "Spectronaut" = 2),
selected = 1)
)
),
hr(),
fluidRow(align="left",
column(width=3, offset =1,
checkboxInput("checkbox_tmt", label = "SPQC Normalized TMT sets"),
checkboxInput("checkbox_isoform", label = "Use Peptide Isoform?"),
),
column(width=3, offset =1,
checkboxInput("checkbox_norm_ptm", label = "Normalize on PTM?"),
textInput("peptide_norm_grep", label="Normalize PTM grep", value = "Enter value here")
),
column(width=3, offset = 1,
checkboxInput("checkbox_impute_ptm", label = "Impute Distribution based on PTM?"),
textInput("peptide_impute_grep", label="Impute PTM grep", value = "Enter value here")
)
),
fluidRow(
selectInput("razor", label = h5("Peptides to Use"),
choices = list("Razor", "Unique", "Shared"),
selected = "Razor")
),
hr(),
fluidRow(
textInput("fileprefix", label="Enter file prefix for data output", value = "Enter value here"),
shinyFilesButton('raw_files', label='Select PD Text Export Files', title='Please select raw data files', multiple=TRUE,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
br(),
br(),
actionButton("load_data", label = "Load Data File(s)",
style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
), #end tab panel
tabPanel("Overview", value = "tp_overview",
hr(),
fluidRow(
column(width=3, offset =1,
imageOutput("mass_accuracy"),
imageOutput("inj_summary"),
imageOutput("peptide_MZ"),
imageOutput("faims_psm_cv"),
imageOutput("peptide_PI"),
imageOutput("peptide_cruc")
),
column(width=3, offset =1,
imageOutput("peptide_RT"),
imageOutput("feature_width"),
imageOutput("peptide_Charge"),
imageOutput("peptide_aainfo"),
imageOutput("peptide_ai")
),
column(width=3, offset =1,
rHandsontableOutput("project_overview")
)
)
),
tabPanel("Filters", value = "tp_filters", align="center",
tags$h1("Apply Raw Filters"),
hr(),
fluidRow(
column(width=3, offset = 1,
fluidRow(align = "left",
textOutput("text1"),
tags$head(tags$style("#text1{color: blue; font-size: 16px; font-style: bold;}")),
textOutput("text2"),
tags$head(tags$style("#text2{color: blue; font-size: 16px; font-style: bold;}")),
textOutput("text3"),
tags$head(tags$style("#text3{color: blue; font-size: 16px; font-style: bold;}")),
textOutput("text4"),
tags$head(tags$style("#text4{color: blue; font-size: 16px; font-style: bold;}"))
)
),
column(width=6, offset = 1,
fluidRow(align = "left",
numericInput("minimum_measured_all", label="Enter minimum # measured values (all samples)", value = 2),
hr(),
checkboxInput("checkbox_require_x", label = "Require X% measured values in at least one group"),
numericInput("require_x_cutoff", label="Enter X% measured values (decimal)", value = 0.8),
hr(),
checkboxInput("checkbox_filtercv", label = "Filter on Specific Group CV"),
selectInput("text_filtercvgroup", label="Enter group for CV filter",
choices = list("SPQC"), selected = "SPQC"),
numericInput("number_filtercvcutoff", label="Enter CV% for cutoff", value = "Enter value here"),
hr(),
br(),
actionButton("filter_apply", label = "Apply Filters", width = 300,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
)
)
), #end tab panel
tabPanel("Normalize", value = "tp_normalize",
fluidRow(
column(width=4, offset =1,
br(),
hr(),
textOutput("text_f1"),
tags$head(tags$style("#text_f1{color: blue; font-size: 20px; font-style: bold;}")),
checkboxInput("checkbox_norm_include", label = "Include only grep for norm"),
textInput("include_norm_grep", label="Filter Include grep", value = "Enter value here"),
checkboxInput("checkbox_norm_exclude", label = "Exclude grep from norm"),
textInput("exclude_norm_grep", label="Filter Exclude grep", value = "Enter value here"),
actionButton("include_exclude", label = "Apply Filter", width = 300,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
br(),
hr(),
textOutput("text_n1"),
tags$head(tags$style("#text_n1{color: blue; font-size: 20px; font-style: bold;}")),
checkboxInput("checkbox_n1", label = "Sample Loading - Total", value = TRUE),
checkboxInput("checkbox_n2", label = "Trimmed Mean - 10%"),
checkboxInput("checkbox_n3", label = "SL TMM"),
checkboxInput("checkbox_n4", label = "Quantile"),
checkboxInput("checkbox_n5", label = "Linear Regression"),
checkboxInput("checkbox_n6", label = "LOESS"),
checkboxInput("checkbox_n7", label = "VSN"),
checkboxInput("checkbox_n8", label = "Median of Total Intensity"),
checkboxInput("checkbox_n9", label = "Median Intensity"),
checkboxInput("checkbox_n10", label = "Average Intensity"),
checkboxInput("checkbox_n11", label = "Protein"),
textInput("protein_norm_list", label="Protein Norm List", value = "Enter value here"),
br(),
actionButton("norm1", label = "Apply Normalization", width = 300,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
hr()
),
column(width=7, offset =0,
"Raw Data Total Intensity",
br(),
fluidRow(
imageOutput("raw_bar"),
),
br(),
br(),
br(),
br(),
br(),
br(),
br(),
fluidRow(
imageOutput("norm_data_bar")
)
)
)
),
tabPanel("Impute", value = "tp_impute",
fluidRow(
column(width=4, offset =1,
textOutput("text_i1"),
tags$head(tags$style("#text_i1{color: blue; font-size: 20px; font-style: bold;}")),
br(),
radioButtons("radio_impute", label=NULL,
choices = list("Duke/BottomX" = 1, "Floor" = 2, "Minimum" = 3, "Average/Group" = 4,
"Average/Global" = 9, "KNN"= 5, "LocalLeastSquares" = 6, "MLE" = 7, "BottomX" = 8
),
selected = 1),
dropdownButton(
numericInput("impute_floor", label="Impute Floor Intensity", value = "Enter value here"),
numericInput("missing_cutoff", label="%minimum measured values in group to allow missing values to be imputed in measured range", value = 50, width = '100%'),
checkboxInput("checkbox_misaligned", label = "Misaligned Filter"),
numericInput("misaligned_cutoff", label="%missing values to be considered for misalignment if average > intensity cutoff", value = 50, width='100%'),
numericInput("intensity_cutoff_mean_sd", label="#standard deviations (+/-) from mean for intensity cuttof", value = -0.5, width = '100%'),
textOutput("text_i2"),
br(),
actionButton("adjust_intensity_cutoff", label = "Calc Intensity Cutoff", width = 300,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
textOutput("text_impute_ptm"),
br(),
numericInput("bottom_x", label="Bottom X%", value = "5"),
circle = TRUE, status = "info", icon = icon("gear"), width = "500px", size = "sm",
tooltip = tooltipOptions(title = "More Imputation Options")
),
hr(),
actionButton("impute1", label = "Apply Imputation", width = 300,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
),
column(width=7, offset =0,
"Total Intensity Histogram",
br(),
imageOutput("histogram"),
br(),
br(),
br(),
br(),
br(),
br(),
imageOutput("ptm_histogram")
)
)
), #end tab panel
tabPanel("TMT SPQC", value = "tp_tmt",
fluidRow(
column(width=2, offset =0,
numericInput("tmt_sets", label="TMT Sets for IRS Normalization", value = "Enter value here"),
numericInput("tmt_channels", label="TMT Channels", value = "Enter value here"),
checkboxInput("checkbox_tmt_filter", label = "Filter peptides by stdev of average %CV"),
numericInput("tmt_filter_sd", label="Stdev for filter", value = "Enter value here"),
br(),
numericInput("TMT_SPQC_bottom_x", label="Bottom X%", value = "5"),
hr(),
actionButton("tmt_irs_go", label = "Apply IRS Norm", width = 200,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
hr(),
actionButton("tmt_irs_qc", label = "Start Data QC", width = 200,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
),
column(width=5, offset =0,
br(),
br(),
br(),
br(),
br(),
"Total Intensity Histogram",
br(),
imageOutput("histogram_tmt")
),
column(width=5, offset =0,
selectInput("tmt_step", label = h5("TMT IRS Step Barplot"),
choices = list("Step0", "Step1", "Step2", "Step3", "Step4", "Step5", "Step6", "Step7", "Final"),
selected = "Step0"),
br(),
imageOutput("tmt_sl")
)
)
), #end tab panel
tabPanel("QC", value="tp_qc",
navbarPage("QC:", id ="np5",
tabPanel("CV",
rHandsontableOutput("data_CV"),
br(),
imageOutput("cv_plot")
),
tabPanel("ADH",
imageOutput("adh_plot"),
br(),
imageOutput("adh_boxplot")
),
tabPanel("Protein Spike",
fluidRow(
column(width=6, offset =0,
rHandsontableOutput("data_proteinQC")
),
column(width=3, offset =0,
textInput("protein_spike_list", label="Protein Spike Accession(s)")
),
column(width=3, offset =0,
actionButton("calc_protein_spike", label = "Recalculate Protein Spike", width = 200,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
),
hr(),
fluidRow(
column(width=2, offset =0,
selectInput("norm_type", label = h5("Normalization Type"),
choices = list("Choice 1" = 1, "Choice 2" = 2, "Choice 3" = 3),
selected = 1)),
column(width=10, offset =0,
imageOutput("qc_spike_plot"))
),
hr(),
fluidRow(
rHandsontableOutput("protein_qc_spike_levels"),
hr(),
actionButton("update_qc_spike_levels", label = "Save Table", width = 100,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
),
tabPanel("Norm Comparison",
fluidRow(
column(width=2, offset =0,
selectInput("plot_select", label = NULL,
choices = list("barplot", "boxplot"),
selected = "barplot"),
checkboxInput("checkbox_nc1", label = "Sample Loading - Total"),
checkboxInput("checkbox_nc2", label = "Trimmed Mean - 10%"),
checkboxInput("checkbox_nc3", label = "SL TMM"),
checkboxInput("checkbox_nc4", label = "Quantile"),
checkboxInput("checkbox_nc5", label = "Linear Regression"),
checkboxInput("checkbox_nc6", label = "LOESS"),
checkboxInput("checkbox_nc7", label = "VSN"),
checkboxInput("checkbox_nc8", label = "Median of Total Intensity"),
checkboxInput("checkbox_nc9", label = "Median Intensity"),
checkboxInput("checkbox_nc10", label = "Average Intensity"),
checkboxInput("checkbox_nc11", label = "Protein")
),
column(width=4, offset =0,
imageOutput("impute_plot"),
br(),
imageOutput("sl_plot"),
br(),
imageOutput("quantile_plot"),
br(),
imageOutput("lr_plot"),
br(),
imageOutput("ai_plot"),
br(),
imageOutput("mi_plot")
),
column(width=4, offset =1,
imageOutput("sltmm_plot"),
br(),
imageOutput("tmm_plot"),
br(),
imageOutput("vsn_plot"),
br(),
imageOutput("loess_plot"),
br(),
imageOutput("ti_plot"),
br(),
imageOutput("protein_plot")
)
)),
tabPanel("Selected Proteins",
fluidRow(
column(width=2, offset =0,
div(style = "font-size:12px;",
selectInput("protein_select", label = "Select barplot type",
choices = list("ADH", "BiraA", "Bait", "Carbox", "Avidin",
"Protein1", "Protein2", "Protein3", "Protein4"),
selected = "ADH"),
textInput("adh_list", label="ADH Accession"),
textInput("bait_list", label="Bait Accession"),
textInput("avidin_list", label="Avidin Accession"),
textInput("carbox_list", label="Carbox Accession"),
textInput("bira_list", label="BirA Accession"),
textInput("protein1_list", label="Protein1 Accession"),
textInput("protein2_list", label="Protein2 Accession"),
textInput("protein3_list", label="Protein3 Accession"),
textInput("protein4_list", label="Protein4 Accession")
),
actionButton("protein_select_plots", label = "Create/Display Plots", width = 300,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
),
column(width=4, offset =0,
imageOutput("impute_plot_select"),
br(),
imageOutput("sl_plot_select"),
br(),
imageOutput("quantile_plot_select"),
br(),
imageOutput("lr_plot_select"),
br(),
imageOutput("ai_plot_select"),
br(),
imageOutput("mi_plot_select")
),
column(width=4, offset =1,
imageOutput("sltmm_plot_select"),
br(),
imageOutput("tmm_plot_select"),
br(),
imageOutput("vsn_plot_select"),
br(),
imageOutput("loess_plot_select"),
br(),
imageOutput("ti_plot_select"),
br(),
imageOutput("protein_plot_select")
)
)),
tabPanel("One Protein",
fluidRow(
column(width=2, offset =0,
selectInput("select_oneprotein_norm", label = "Normalization", width = 150,
choices = list("Choice 1" = 1, "Choice 2" = 2, "Choice 3" = 3),
selected = 1)
),
column(width=1, offset =0,
textInput("oneprotein_accession", label="Accession", value = "0", width = 100)
),
column(width=1, offset =0,
actionButton("oneprotein_show", label = "Show Graph", width = 100,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
),
fluidRow(
hr(),
column(width=4, offset =1,
imageOutput("oneprotein_plot_select")
),
column(width=4, offset =1,
rHandsontableOutput("oneprotein_stats")
)
)),
tabPanel("One Peptide",
fluidRow(
column(width=2, offset =0,
selectInput("select_onepeptide_norm", label = "Normalization", width = 150,
choices = list("Choice 1" = 1, "Choice 2" = 2, "Choice 3" = 3),
selected = 1)
),
column(width=1, offset =0,
textInput("onepeptide_sequence", label="Sequence", value = "0", width = 100)
),
column(width=1, offset =0,
actionButton("onepeptide_show", label = "Show Graph", width = 100,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
),
fluidRow(
hr(),
column(width=4, offset =1,
imageOutput("onepeptide_plot_select")
),
column(width=4, offset =1,
rHandsontableOutput("onepeptide_stats")
)
)),
tabPanel("Data", value = "tp10",
fluidRow(
column(width=2, offset =0,
selectInput("select_final_data", label = "Normalization", width = 150,
choices = list("Choice 1" = 1, "Choice 2" = 2, "Choice 3" = 3),
selected = 1)
),
column(width=1, offset =0,
numericInput("data_topn", label="TopN", value = 0, width = 100)
),
column(width=1, offset =0,
textInput("data_accession", label="Accession", value = "0", width = 100)
),
column(width=1, offset =0,
textInput("data_description", label="Description", value = "0", width = 100)
),
column(width=1, offset =0,
actionButton("data_show", label = "Filter Data", width = 100,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
),
fluidRow(
hr(),
tags$head(tags$style("#data_final{color: blue;
font-size: 12px;
}"
)
),
rHandsontableOutput("data_final")
)
)
) #end of qc navbarpage
), #end of qc tabpanel
tabPanel("Load Data", value = "tp_customer_load", align="center",
hr(),
tags$h1("Welcome to DPMSR Proteome Discoverer Data Visualization Tool"),
br(),
br(),
br(),
br(),
tags$h2("Choose and Load the study design file..."),
br(),
fileInput("customer_dpmsr_set", "Choose dpmsr_set file",
multiple = FALSE,
accept = c(".dpmsr_set", ".txt")),
br(),
br(),
br(),
actionButton("load_customer_dpmsr_set", label = "Load dpmsr_set", width = 200,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
br(),
br(),
br(),
br(),
br(),
span(textOutput("app_version_text2"), style="color:blue; font-size:16px"),
),
tabPanel("Stats", value = "tp_stats",
navbarPage("Stats:", id ="nbp_stats",
tabPanel("Design", id="tp_stats_design",
fluidRow(
column(width=12, offset =0,
hr(),
tags$head(tags$style("#stats_design_table{color: blue;
font-size: 12px;
}"
)
),
DT::dataTableOutput("stats_design_table", width='100%')
)
)
),
tabPanel("Setup", id="tp_stats_setup",
fluidRow(
column(width=1, offset =0,
selectInput("comp_number", label = "Comp #", width = 150,
choices = list(1,2,3,4,5,6,7,8,9,10,11,12),
selected = 1)
),
column(width=1, offset =0,
selectInput("select_final_data_stats", label = "Normalization", width = 150,
choices = list("Choice 1" = 1, "Choice 2" = 2, "Choice 3" = 3),
selected = 1)
),
column(width=1, offset =0,
numericInput("pvalue_cutoff", label="pvalue cutoff", value = .05)
),
column(width=1, offset =0,
numericInput("foldchange_cutoff", label="FC cutoff", value = 2)
),
column(width=2, offset =0,
numericInput("missing_factor", label="Measured % (decimal)", value = 0.6)
),
column(width=2, offset =0,
pickerInput(inputId = "comp_spqc", label = "SPQC Group?", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 3"), multiple = TRUE
)
),
column(width=1, offset =0,
dropdownButton(
textOutput("stats_gear1"),
checkboxInput("peptide_missing_filter", label = "Refilter peptides by requiring X% measured values in one group?"),
numericInput("peptide_missing_factor", label="Peptide X% measured cutoff (decimal)", value = 0.8),
checkboxInput("peptide_cv_filter", label = "Refilter peptides by requiring X %CV one group?"),
numericInput("peptide_cv_factor", label="Peptide X CV% cutoff", value = 100),
textOutput("stats_gear2"),
checkboxInput("stats_spqc_cv_filter", label = "Filter by SPQC CV"),
numericInput("stats_spqc_cv_filter_factor", label="SPQC %CV Cutoff", value = 50),
checkboxInput("stats_comp_cv_filter", label = "Require one group CV below cuttoff"),
numericInput("stats_comp_cv_filter_factor", label="Comp %CV Cutoff", value = 50),
checkboxInput("pair_comp", label = "Pairwise Comparisons"),
checkboxInput("stats_peptide_minimum", label = "Require minimum # of peptides per protein", value = 0),
numericInput("stats_peptide_minimum_factor", label="Peptide Minimum", value = 1),
h5('Extra Stats'),
checkboxInput("checkbox_adjpval", label = "Include adjusted pvalue?"),
selectInput("padjust_options", label = "p.adjust method", choices = list("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr"),
selected = "bonferroni"),
checkboxInput("checkbox_filter_adjpval", label = "Filter with adjusted pvalue?"),
checkboxInput("checkbox_cohensd", label = "Include Cohen's D?"),
checkboxInput("checkbox_cohensd_hedges", label = "Use Hedge's Correction (low N)?"),
checkboxInput("checkbox_limmapvalue", label = "Include Limma Pvalue?"),
h5('Final Excel Options'),
checkboxInput("checkbox_report_ptm", label = "Report Only PTM?"),
textInput("peptide_report_grep", label="Report PTM grep", value = "Enter value here"),
checkboxInput("checkbox_report_accession", label = "Report Specific Accession(s) Only"),
textInput("report_accession", label="Protein Accessions for Final Report", value = "Enter value"),
checkboxInput("checkbox_add_gene_column", label = "Add gene name column"),
circle = TRUE, status = "info", icon = icon("gear"), width = "300px", size = "sm",
tooltip = tooltipOptions(title = "Click to see more options!")
)
),
column(width=2, offset =0,
textInput("final_stats_name", label="Final Stats Excel Name",
value = str_c("Final_CompHere_stats.xlsx"))
)
),
hr(),
fluidRow(
column(width=2, offset =0,
span(textOutput("comp1_text"), style="color:blue; font-size:20px"),
pickerInput(inputId = "comp_1N", label = "Numerator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
pickerInput(inputId = "comp_1D", label = "Denominator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
textInput("comp1_name", label="Description", value = "")
),
column(width=2, offset =0,
span(textOutput("comp2_text"), style="color:blue; font-size:20px"),
pickerInput(inputId = "comp_2N", label = "Numerator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
pickerInput(inputId = "comp_2D", label = "Denominator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
textInput("comp2_name", label="Description", value = "")
),
column(width=2, offset =0,
span(textOutput("comp3_text"), style="color:blue; font-size:20px"),
pickerInput(inputId = "comp_3N", label = "Numerator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
pickerInput(inputId = "comp_3D", label = "Denominator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
textInput("comp3_name", label="Description", value = "")
),
column(width=2, offset =0,
span(textOutput("comp4_text"), style="color:blue; font-size:20px"),
pickerInput(inputId = "comp_4N", label = "Numerator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
pickerInput(inputId = "comp_4D", label = "Denominator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
textInput("comp4_name", label="Description", value = "")
) ,
column(width=2, offset =0,
span(textOutput("comp5_text"), style="color:blue; font-size:20px"),
pickerInput(inputId = "comp_5N", label = "Numerator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
pickerInput(inputId = "comp_5D", label = "Denominator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
textInput("comp5_name", label="Description", value = "")
),
column(width=2, offset =0,
span(textOutput("comp6_text"), style="color:blue; font-size:20px"),
pickerInput(inputId = "comp_6N", label = "Numerator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
pickerInput(inputId = "comp_6D", label = "Denominator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
textInput("comp6_name", label="Description", value = "")
)
),
fluidRow(
hr()
),
fluidRow(
column(width=2, offset =0,
span(textOutput("comp7_text"), style="color:blue; font-size:20px"),
pickerInput(inputId = "comp_7N", label = "Numerator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
pickerInput(inputId = "comp_7D", label = "Denominator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
textInput("comp7_name", label="Description", value = "")
),
column(width=2, offset =0,
span(textOutput("comp8_text"), style="color:blue; font-size:20px"),
pickerInput(inputId = "comp_8N", label = "Numerator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
pickerInput(inputId = "comp_8D", label = "Denominator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
textInput("comp8_name", label="Description", value = "")
),
column(width=2, offset =0,
span(textOutput("comp9_text"), style="color:blue; font-size:20px"),
pickerInput(inputId = "comp_9N", label = "Numerator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
pickerInput(inputId = "comp_9D", label = "Denominator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
textInput("comp9_name", label="Description", value = "")
),
column(width=2, offset =0,
span(textOutput("comp10_text"), style="color:blue; font-size:20px"),
pickerInput(inputId = "comp_10N", label = "Numerator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
pickerInput(inputId = "comp_10D", label = "Denominator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
textInput("comp10_name", label="Description", value = "")
) ,
column(width=2, offset =0,
span(textOutput("comp11_text"), style="color:blue; font-size:20px"),
pickerInput(inputId = "comp_11N", label = "Numerator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
pickerInput(inputId = "comp_11D", label = "Denominator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
textInput("comp11_name", label="Description", value = "")
),
column(width=2, offset =0,
span(textOutput("comp12_text"), style="color:blue; font-size:20px"),
pickerInput(inputId = "comp_12N", label = "Numerator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
pickerInput(inputId = "comp_12D", label = "Denominator", choices = "None",
options = list(`actions-box` = TRUE,size = 10,
`selected-text-format` = "count > 7"), multiple = TRUE
),
textInput("comp12_name", label="Description", value = "")
)
),
fluidRow(align="center",
hr(),
#rHandsontableOutput("stat2_table"),
tags$head(tags$style("#stat2_N_1{color: blue; font-size: 16px; font-style: bold;}")),
actionButton("check_stats", label = "Set Comparisons", width = 300,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
br(),
br(),
actionButton("start_stats", label = "Start Anlaysis", width = 300,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
br(),
br(),
actionButton("save_stats", label = "Create Excel Output File", width = 300,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
br(),
br(),
downloadButton('download_stats_excel')
)
),
tabPanel("Graphs", id="tp_stats_graph1",
fluidRow(
column(width=3, offset =0,
pickerInput(inputId = "stats_plot_comp", label = "Comparison(s) to plot", choices = "None",
options = list(`actions-box` = TRUE, size = 100,
`selected-text-format` = "count > 5"), multiple = TRUE)
),
column(width=2, offset =0,
checkboxInput("stats_plot_spqc", label = "Add SPQC?")
),
column(width=4, offset =0,
actionButton("create_stats_plots", label = "Create Plots", width = 100,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
),
fluidRow(
column(width=6, offset =0,
dropdownButton(
textInput("stats_barplot_y_axis_label", label="y axis label", value = "Intensity", width = 200),
textInput("stats_barplot_title", label="plot title", value = "Total Summed Intensity", width = 200),
sliderInput("stats_barplot_label_size", label = h5("Label Size"), min = 1,
max = 50, value = 11),
sliderInput("stats_barplot_title_size", label = h5("Title Size"), min = 10,
max = 50, value = 20),
circle = TRUE, status = "danger", icon = icon("gear"), width = "300px", size = "sm",
tooltip = tooltipOptions(title = "Click to see inputs !")
),
div(
style = "position:relative",
plotOutput("stats_barplot", width = 600, height = 400)
),
downloadButton('download_stats_barplot')
),
column(width=6, offset =0,
dropdownButton(
textInput("stats_boxplot_y_axis_label", label="y axis label", value = "Intensity", width = 200),
textInput("stats_boxplot_title", label="plot title", value = "Total Summed Intensity", width = 200),
sliderInput("stats_boxplot_label_size", label = h5("Label Size"), min = 1,
max = 50, value = 11),
sliderInput("stats_boxplot_title_size", label = h5("Title Size"), min = 10,
max = 50, value = 20),
circle = TRUE, status = "danger", icon = icon("gear"), width = "300px", size = "sm",
tooltip = tooltipOptions(title = "Click to see inputs !")
),
div(
style = "position:relative",
plotOutput("stats_boxplot", width = 600, height = 400)
),
downloadButton('download_stats_boxplot')
)
),
hr(),
fluidRow(
column(width=6, offset =0,
dropdownButton(
selectInput("stats_pca2d_x", label = "pca xaxis", choices = list("PC1", "PC2", "PC3", "PC4", "PC5"),
selected = "PC1"),
selectInput("stats_pca2d_y", label = "pca yaxis", choices = list("PC1", "PC2", "PC3", "PC4", "PC5"),
selected = "PC2"),
textInput("stats_pca2d_title", label="plot title", value = "pca2d", width = 200),
sliderInput("stats_pca2d_label_size", label = h5("Label Size"), min = 1,
max = 50, value = 11),
sliderInput("stats_pca2d_title_size", label = h5("Title Size"), min = 10,
max = 50, value = 20),
sliderInput("stats_pca2d_dot_size", label = h5("Point Size"), min = 1,
max = 20, value = 4),
circle = TRUE, status = "danger", icon = icon("gear"), width = "300px", size = "sm",
tooltip = tooltipOptions(title = "Click to see inputs !")
),
div(
style = "position:relative",
plotOutput("stats_pca2d", width = 600, height = 400,
hover = hoverOpts("plot_pca2d_hover", delay = 100, delayType = "debounce")),
uiOutput("hover_pca2d_info")
),
downloadButton('download_stats_pca2d')
),
column(width=6, offset =0,
dropdownButton(
textInput("stats_pca3d_title", label="plot title", value = "pca3d", width = 200),
sliderInput("stats_pca3d_label_size", label = h5("Label Size"), min = 1,
max = 50, value = 11),
sliderInput("stats_pca3d_title_size", label = h5("Title Size"), min = 10,
max = 50, value = 20),
sliderInput("stats_pca3d_dot_size", label = h5("Point Size"), min = 1,
max = 10, value = 2),
circle = TRUE, status = "danger", icon = icon("gear"), width = "300px", size = "sm",
tooltip = tooltipOptions(title = "Click to see inputs !")
),
div(
style = "position:relative",
rglwidgetOutput("stats_pca3d", width = 600, height = 400)
),
downloadButton('download_stats_pca3d')
)
),
hr(),
fluidRow(
column(width=6, offset =0,
dropdownButton(
textInput("stats_cluster_title", label="plot title", value = "cluster", width = 200),
sliderInput("stats_cluster_label_size", label = h5("Label Size"), min = 1,
max = 50, value = 11),
sliderInput("stats_cluster_title_size", label = h5("Title Size"), min = 10,
max = 50, value = 20),
colourpicker::colourInput("cluster_high_color", "Select High Color", "#FF3366"),
colourpicker::colourInput("cluster_low_color", "Select Low Color", "#009933"),
circle = TRUE, status = "danger", icon = icon("gear"), width = "300px", size = "sm",
tooltip = tooltipOptions(title = "Click to see inputs !")
),
div(
style = "position:relative",
plotOutput("stats_cluster", width = 600, height = 400)
),
downloadButton('download_stats_cluster')
),
column(width=6, offset =0,
dropdownButton(
textInput("stats_heatmap_title", label="plot title", value = "heatmap", width = 200),
circle = TRUE, status = "danger", icon = icon("gear"), width = "300px", size = "sm",
tooltip = tooltipOptions(title = "Click to see inputs !")
),
div(
style = "position:relative",
plotOutput("stats_heatmap", width = 600, height = 400)
),
downloadButton('download_stats_heatmap')
)
)
), # end graphs
tabPanel("Volcano", id="tp_stats_volcano",
fluidRow(
column(width=3, offset =0,
actionButton("create_stats_volcano", label = "Create Volcano Plots", width = 300,
style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
),
column(width=2, offset = 0,
textInput("volcano_highlight", label = "Highlight search term (description)")
),
column(width=1, offset =0,
dropdownButton(
h3('Highlight Proteins'),
h5('Enter list of strings to search in protein descriptions.'),
h5('Beware of extra trailing spaces'),
h5('Search is NOT case sensitive'),
colourpicker::colourInput("volcano_highlight_color", "Description Highlight Color", "red"),
checkboxInput("stats_volcano_highlight_up", label = "Highlight stat signif up?", value = TRUE),
checkboxInput("stats_volcano_highlight_down", label = "Highlight stat signif down?", value = TRUE),
colourpicker::colourInput("volcano_highlight_color_up", "Stat 'Down' Color", "red"),
colourpicker::colourInput("volcano_highlight_color_down", "Stat 'Up' Color", "red"),
sliderInput("volcano_highlight_dot_size", label = h5("Point Size"), min = 1,
max = 10, value = 3),
sliderInput("volcano_highlight_alpha", label = h5("Transparency"), min = 0.1,
max = 1, value = 0.5),
circle = TRUE, status = "danger", icon = icon("gear"), width = "300px", size = "sm",
tooltip = tooltipOptions(title = "Click for help on Volcano protein highlights")
)
),
column(width=3, offset = 0,
checkboxInput("stats_volcano_fixed_axis", label = "Fix x and y axis for all plots?"),
checkboxInput("stats_volcano_highlight_signif", label = "Highlight statistically signifigant?")
),
column(width=1, offset = 0,