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added loading animations
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@Hailey-Z
Hailey-Z committed Oct 24, 2022
1 parent 57347f1 commit f074394
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Showing 3 changed files with 67 additions and 45 deletions.
1 change: 1 addition & 0 deletions global.R
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ library("shinyWidgets")# new added
library("ggVennDiagram") # new added
library("rhandsontable") # new added
library("shinyBS") # new added
library("shinycssloaders") # new added

conflict_prefer("box", "shinydashboard")
conflict_prefer("select", "dplyr")
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14 changes: 13 additions & 1 deletion server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -996,12 +996,24 @@ server <- function(input, output, session) {
})

## Enrichment Outputs
output$spinner_go <- renderUI({
req(input$go_analysis)
shinycssloaders::withSpinner(plotOutput("go_enrichment"), color = "#3c8dbc")
})

output$go_enrichment<-renderPlot({
Sys.sleep(2)
go_input()$plot_go
})

output$spinner_pa <- renderUI({
req(input$pathway_analysis)
shinycssloaders::withSpinner(plotOutput("pathway_enrichment"), color = "#3c8dbc")
})

output$pathway_enrichment<-renderPlot({
pathway_input()$plot_pa
Sys.sleep(2)
pathway_input()$plot_pa
})

##### Download Functions
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97 changes: 53 additions & 44 deletions ui.R
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Original file line number Diff line number Diff line change
Expand Up @@ -240,7 +240,8 @@ ui <- function(request){shinyUI(
fluidRow(id="results_tab",
box(
title = "Results Table",
DT::dataTableOutput("contents"),
shinycssloaders::withSpinner(DT::dataTableOutput("contents"),
color = "#3c8dbc"),
# actionButton("clear", "Deselect Rows"),
actionButton("original", "Refresh Table"),
width = 6,
Expand All @@ -259,7 +260,7 @@ ui <- function(request){shinyUI(
width = 12,
tabPanel(title = "Volcano plot",
fluidRow(
box(uiOutput("volcano_cntrst"), width = 4),
box(uiOutput("volcano_cntrst"), width = 5),
box(numericInput("fontsize",
"Font size",
min = 0, max = 8, value = 4),
Expand All @@ -279,19 +280,19 @@ ui <- function(request){shinyUI(
),

fluidRow(
plotOutput("volcano", height = 600,
shinycssloaders::withSpinner(plotOutput("volcano", height = 600,
# hover = "protein_hover"),
#),
# click = "protein_click"),
brush = "protein_brush",
click = "protein_click"),
click = "protein_click"), color = "#3c8dbc"),
downloadButton('downloadVolcano', 'Save Highlighted Plot'),
actionButton("resetPlot", "Clear Selection")
#)),
)),
tabPanel(title= "Heatmap",
fluidRow(
plotOutput("heatmap", height = 600)
shinycssloaders::withSpinner(plotOutput("heatmap", height = 600), color = "#3c8dbc")
),
fluidRow(
box(numericInput("cluster_number",
Expand Down Expand Up @@ -322,7 +323,7 @@ ui <- function(request){shinyUI(
protein intesities across conditions and replicates")
),
fluidRow(
plotOutput("protein_plot"),
shinycssloaders::withSpinner(plotOutput("protein_plot"), color = "#3c8dbc"),
downloadButton('downloadProtein', 'Download Plot')
)
)
Expand Down Expand Up @@ -370,38 +371,38 @@ ui <- function(request){shinyUI(
width=6,
tabBox(title = "QC Plots", width = 12, id="qc_tabBox", height=700,
tabPanel(title = "PCA Plot",
plotlyOutput("pca_plot", height=600)
shinycssloaders::withSpinner(plotlyOutput("pca_plot", height=600), color = "#3c8dbc")
# downloadButton('download_pca_svg', "Save svg")
),
tabPanel(title="Sample Correlation",
plotOutput("sample_corr", height = 600),
shinycssloaders::withSpinner(plotOutput("sample_corr", height = 600), color = "#3c8dbc"),
downloadButton('download_corr_svg', "Save svg")
),
tabPanel(title= "Sample CVs",
plotOutput("sample_cvs", height = 600),
shinycssloaders::withSpinner(plotOutput("sample_cvs", height = 600), color = "#3c8dbc"),
downloadButton('download_cvs_svg', "Save svg")
),
# conditionalPanel(condition="input.exp != 'TMT'",
tabPanel(title = "Protein Numbers",
plotOutput("numbers", height = 600),
shinycssloaders::withSpinner(plotOutput("numbers", height = 600), color = "#3c8dbc"),
downloadButton('download_num_svg', "Save svg")),
# conditionalPanel(condition="input.exp != 'TMT'",
tabPanel(title = "Sample coverage", value="sample_coverage_tab",
plotOutput("coverage", height = 600),
shinycssloaders::withSpinner(plotOutput("coverage", height = 600), color = "#3c8dbc"),
downloadButton('download_cov_svg', "Save svg")),
tabPanel(title = "Normalization", value="norm_tab",
plotOutput("norm", height = 600),
shinycssloaders::withSpinner(plotOutput("norm", height = 600), color = "#3c8dbc"),
downloadButton('download_norm_svg', "Save svg")
),
# tabPanel(title = "Missing values - Quant",
# plotOutput("detect", height = 600)
# ),
tabPanel(title = "Missing values - Heatmap",
plotOutput("missval", height = 600),
shinycssloaders::withSpinner(plotOutput("missval", height = 600), color = "#3c8dbc"),
downloadButton('download_missval_svg', "Save svg")
),
tabPanel(title = "Imputation", value="imputation_tab",
plotOutput("imputation", height = 600),
shinycssloaders::withSpinner(plotOutput("imputation", height = 600), color = "#3c8dbc"),
downloadButton('download_imp_svg', "Save svg")
)#,
# tabPanel(title = "p-value Histogram",
Expand All @@ -413,36 +414,44 @@ ui <- function(request){shinyUI(
width=6,
tabBox(title = "Enrichment", width = 12, height=600,
tabPanel(title="Gene Ontology",
box(uiOutput("contrast"), width = 4),
box(selectInput("go_database", "GO database:",
c("Molecular Function"="GO_Molecular_Function_2021",
"Cellular Component"="GO_Cellular_Component_2021",
"Biological Process"="GO_Biological_Process_2021")),
width= 4),
box(radioButtons("go_direction",
"Direction",
choices = c("Up"="UP", "Down"="DOWN"),
selected = "UP"), width = 2),
actionButton("go_analysis", "Run Enrichment"),
box(plotOutput("go_enrichment", height=500),
width=12),
downloadButton('downloadGO', 'Download Table')
fluidRow(
column(4,uiOutput("contrast")),
column(4, selectInput("go_database", "GO database:",
c("Molecular Function"="GO_Molecular_Function_2021",
"Cellular Component"="GO_Cellular_Component_2021",
"Biological Process"="GO_Biological_Process_2021"))),
column(2, radioButtons("go_direction",
"Direction",
choices = c("Up"="UP", "Down"="DOWN"),
selected = "UP")),
column(12, actionButton("go_analysis", "Run Enrichment")),
column(12,
box(width = 12, uiOutput("spinner_go"),height = 500)
),
column(12,
downloadButton('downloadGO', 'Download Table')
)
)
),
tabPanel(title= "Pathway enrichment",
box(uiOutput("contrast_1"), width = 4),
box(selectInput("pathway_database", "Pathway database:",
c("Hallmark"="MSigDB_Hallmark_2020",
"KEGG"="KEGG_2021_Human",
"Reactome"="Reactome_2022")),
width= 4),
box(radioButtons("pathway_direction",
"Direction",
choices = c("Up"="UP", "Down"="DOWN"),
selected = "UP"), width = 2),
actionButton("pathway_analysis", "Run Enrichment"),
box(plotOutput("pathway_enrichment", height=500),
width=12),
downloadButton('downloadPA', 'Download Table')
fluidRow(
column(4,uiOutput("contrast_1")),
column(4, selectInput("pathway_database", "Pathway database:",
c("Hallmark"="MSigDB_Hallmark_2020",
"KEGG"="KEGG_2021_Human",
"Reactome"="Reactome_2022"))),
column(2, radioButtons("pathway_direction",
"Direction",
choices = c("Up"="UP", "Down"="DOWN"),
selected = "UP")),
column(12, actionButton("pathway_analysis", "Run Enrichment")),
column(12,
box(width = 12, uiOutput("spinner_pa"),height = 500)
),
column(12,
downloadButton('downloadPA', 'Download Table')
)
)
)
) # Tab box close
) # column end
Expand Down Expand Up @@ -481,7 +490,7 @@ ui <- function(request){shinyUI(
column(9,
box(width = NULL,
title = "Results Table",
DT::dataTableOutput("contents_occ"),
shinycssloaders::withSpinner(DT::dataTableOutput("contents_occ"), color = "#3c8dbc"),
downloadButton('download_attendance', 'Download Table'),
status = "success",
solidHeader = TRUE),
Expand All @@ -494,7 +503,7 @@ ui <- function(request){shinyUI(
box(width = 4,id = "con_2", uiOutput("condition_2")),
box(width = 4,id = "con_3", uiOutput("condition_3"))),
column(12,
plotOutput("venn_plot")),
shinycssloaders::withSpinner(plotOutput("venn_plot"), color = "#3c8dbc")),
column(12, downloadButton('download_venn_svg', "Save svg")),
status = "success",
solidHeader = TRUE)
Expand Down

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