pablo-rodr-bio2 authored on 17/05/2021 17:29:04
| ... | ... |
@@ -12,26 +12,21 @@ dashboardPage( |
| 12 | 12 |
tags$head( |
| 13 | 13 |
tags$link(rel = "stylesheet", type = "text/css", href = "style.css") |
| 14 | 14 |
), |
| 15 |
- fluidRow( |
|
| 16 |
- column( |
|
| 17 |
- width = 12, |
|
| 18 |
- align = "center", |
|
| 19 |
- h3("Data Input", style="font-weight: bold")
|
|
| 20 |
- ) |
|
| 21 |
- ), |
|
| 22 |
- # h3("Data input"),
|
|
| 15 |
+ div(h3("DATA INPUT", style="font-weight: bold"), align = "center"),
|
|
| 16 |
+ br(), |
|
| 23 | 17 |
matrixUI("matrix1"),
|
| 24 | 18 |
br(), |
| 25 | 19 |
geneSetsUI("genes1"),
|
| 26 | 20 |
br(), |
| 27 |
- radioButtons("arg", "Change default settings?",
|
|
| 21 |
+ radioButtons(inputId = "arg", |
|
| 22 |
+ label = h5("CHANGE DEFAULT SETTINGS?", style="font-weight: bold"),
|
|
| 28 | 23 |
c("No" = "no",
|
| 29 | 24 |
"Yes" = "yes")), |
| 30 | 25 |
br(), |
| 31 | 26 |
fluidRow( |
| 32 | 27 |
column( |
| 33 | 28 |
width = 12, align = "left", |
| 34 |
- actionButton("button", "Run", class = "run-btn", icon = icon("play-circle"),
|
|
| 29 |
+ actionButton("button", "RUN", class = "run-btn", icon = icon("play-circle"),
|
|
| 35 | 30 |
width = "10vw"), |
| 36 | 31 |
downloadUI("download"),
|
| 37 | 32 |
closeBtnUI("close")
|
pablo-rodr-bio2 authored on 14/05/2021 09:37:52
| ... | ... |
@@ -24,14 +24,15 @@ dashboardPage( |
| 24 | 24 |
br(), |
| 25 | 25 |
geneSetsUI("genes1"),
|
| 26 | 26 |
br(), |
| 27 |
- radioButtons("arg", "Change default settings:",
|
|
| 27 |
+ radioButtons("arg", "Change default settings?",
|
|
| 28 | 28 |
c("No" = "no",
|
| 29 | 29 |
"Yes" = "yes")), |
| 30 | 30 |
br(), |
| 31 | 31 |
fluidRow( |
| 32 | 32 |
column( |
| 33 | 33 |
width = 12, align = "left", |
| 34 |
- actionButton("button", "Run"),
|
|
| 34 |
+ actionButton("button", "Run", class = "run-btn", icon = icon("play-circle"),
|
|
| 35 |
+ width = "10vw"), |
|
| 35 | 36 |
downloadUI("download"),
|
| 36 | 37 |
closeBtnUI("close")
|
| 37 | 38 |
) |
| ... | ... |
@@ -40,7 +41,7 @@ dashboardPage( |
| 40 | 41 |
|
| 41 | 42 |
dashboardBody( |
| 42 | 43 |
shinyjs::useShinyjs(), |
| 43 |
- add_busy_spinner(spin = "double-bounce", position = "bottom-right", |
|
| 44 |
+ add_busy_spinner(spin = "cube-grid", position = "bottom-right", |
|
| 44 | 45 |
height = "100px", width = "100px"), |
| 45 | 46 |
fluidRow( |
| 46 | 47 |
box( |
| ... | ... |
@@ -50,7 +51,14 @@ dashboardPage( |
| 50 | 51 |
textOutput("errorsGsva"),
|
| 51 | 52 |
htmlOutput("text1"),
|
| 52 | 53 |
plot1_UI("plot1"),
|
| 53 |
- tableOutput("result")
|
|
| 54 |
+ br(), |
|
| 55 |
+ fluidRow( |
|
| 56 |
+ column( |
|
| 57 |
+ width = 12, |
|
| 58 |
+ align = "center", |
|
| 59 |
+ tableOutput("result")
|
|
| 60 |
+ ) |
|
| 61 |
+ ) |
|
| 54 | 62 |
), |
| 55 | 63 |
tabPanel("GeneSets",
|
| 56 | 64 |
uiOutput("text2"),
|
pablo-rodr-bio2 authored on 13/05/2021 11:26:15
| ... | ... |
@@ -29,9 +29,12 @@ dashboardPage( |
| 29 | 29 |
"Yes" = "yes")), |
| 30 | 30 |
br(), |
| 31 | 31 |
fluidRow( |
| 32 |
- actionButton("button", "Run"),
|
|
| 33 |
- downloadUI("download"),
|
|
| 34 |
- closeBtnUI("close"),
|
|
| 32 |
+ column( |
|
| 33 |
+ width = 12, align = "left", |
|
| 34 |
+ actionButton("button", "Run"),
|
|
| 35 |
+ downloadUI("download"),
|
|
| 36 |
+ closeBtnUI("close")
|
|
| 37 |
+ ) |
|
| 35 | 38 |
) |
| 36 | 39 |
), |
| 37 | 40 |
|
pablo-rodr-bio2 authored on 06/05/2021 17:51:11
| ... | ... |
@@ -1,21 +1,25 @@ |
| 1 | 1 |
dashboardPage( |
| 2 | 2 |
title = "GSVA Shiny Application", |
| 3 |
+ |
|
| 3 | 4 |
dashboardHeader( |
| 4 | 5 |
tags$li(class = "dropdown", |
| 5 |
- tags$style(".main-header {max-height: 75px}"),
|
|
| 6 |
- tags$style(".main-header .logo {height: 75px}"),
|
|
| 7 |
- tags$div("GSVA Shiny Application", style = "font-size: 30px;
|
|
| 8 |
- color: white; font-weight: bold;") |
|
| 6 |
+ tags$div(id = "app_title", "GSVA Shiny Application") |
|
| 9 | 7 |
), |
| 10 | 8 |
title = tags$img(src="GSVA.png", height=75, width=75) |
| 11 | 9 |
), |
| 10 |
+ |
|
| 12 | 11 |
dashboardSidebar( |
| 13 |
- tags$style(".left-side, .main-sidebar {padding-top: 75px}"),
|
|
| 14 | 12 |
tags$head( |
| 15 | 13 |
tags$link(rel = "stylesheet", type = "text/css", href = "style.css") |
| 16 | 14 |
), |
| 17 |
- h3("Data input"),
|
|
| 18 |
- #Select data source |
|
| 15 |
+ fluidRow( |
|
| 16 |
+ column( |
|
| 17 |
+ width = 12, |
|
| 18 |
+ align = "center", |
|
| 19 |
+ h3("Data Input", style="font-weight: bold")
|
|
| 20 |
+ ) |
|
| 21 |
+ ), |
|
| 22 |
+ # h3("Data input"),
|
|
| 19 | 23 |
matrixUI("matrix1"),
|
| 20 | 24 |
br(), |
| 21 | 25 |
geneSetsUI("genes1"),
|
| ... | ... |
@@ -23,37 +27,43 @@ dashboardPage( |
| 23 | 27 |
radioButtons("arg", "Change default settings:",
|
| 24 | 28 |
c("No" = "no",
|
| 25 | 29 |
"Yes" = "yes")), |
| 26 |
- actionButton("button", "Run"),
|
|
| 27 | 30 |
br(), |
| 28 |
- downloadUI("download"),
|
|
| 29 |
- closeBtnUI("close")
|
|
| 31 |
+ fluidRow( |
|
| 32 |
+ actionButton("button", "Run"),
|
|
| 33 |
+ downloadUI("download"),
|
|
| 34 |
+ closeBtnUI("close"),
|
|
| 35 |
+ ) |
|
| 30 | 36 |
), |
| 37 |
+ |
|
| 31 | 38 |
dashboardBody( |
| 32 | 39 |
shinyjs::useShinyjs(), |
| 33 | 40 |
add_busy_spinner(spin = "double-bounce", position = "bottom-right", |
| 34 | 41 |
height = "100px", width = "100px"), |
| 35 |
- box( |
|
| 36 |
- width = 9, |
|
| 37 |
- tabsetPanel(id = "Panels", type="tabs", |
|
| 38 |
- tabPanel("Samples",
|
|
| 39 |
- textOutput("errorsGsva"),
|
|
| 40 |
- htmlOutput("text1"),
|
|
| 41 |
- plot1_UI("plot1"),
|
|
| 42 |
- tableOutput("result")
|
|
| 43 |
- ), |
|
| 44 |
- tabPanel("GeneSets",
|
|
| 45 |
- uiOutput("text2"),
|
|
| 46 |
- htmlOutput("text3"),
|
|
| 47 |
- plot2_UI("plot2"),
|
|
| 48 |
- plot3_UI("plot3")
|
|
| 49 |
- ), |
|
| 50 |
- tabPanel("Session Info",
|
|
| 51 |
- verbatimTextOutput("sessionInfo"))
|
|
| 42 |
+ fluidRow( |
|
| 43 |
+ box( |
|
| 44 |
+ width = 9, |
|
| 45 |
+ tabsetPanel(id = "Panels", type="tabs", |
|
| 46 |
+ tabPanel("Samples",
|
|
| 47 |
+ textOutput("errorsGsva"),
|
|
| 48 |
+ htmlOutput("text1"),
|
|
| 49 |
+ plot1_UI("plot1"),
|
|
| 50 |
+ tableOutput("result")
|
|
| 51 |
+ ), |
|
| 52 |
+ tabPanel("GeneSets",
|
|
| 53 |
+ uiOutput("text2"),
|
|
| 54 |
+ htmlOutput("text3"),
|
|
| 55 |
+ plot2_UI("plot2"),
|
|
| 56 |
+ plot3_UI("plot3")
|
|
| 57 |
+ ), |
|
| 58 |
+ tabPanel("Session Info",
|
|
| 59 |
+ verbatimTextOutput("sessionInfo"))
|
|
| 60 |
+ ) |
|
| 61 |
+ ), |
|
| 62 |
+ box( |
|
| 63 |
+ width = 3, |
|
| 64 |
+ argumentsDataUI("argumentsInput")
|
|
| 52 | 65 |
) |
| 53 |
- ), |
|
| 54 |
- box( |
|
| 55 |
- width = 3, |
|
| 56 |
- argumentsDataUI("argumentsInput")
|
|
| 57 | 66 |
) |
| 58 | 67 |
) |
| 68 |
+ |
|
| 59 | 69 |
) |
pablo-rodr-bio2 authored on 05/05/2021 06:01:52
| ... | ... |
@@ -1,64 +1,59 @@ |
| 1 |
-fluidPage( |
|
| 2 |
- theme = shinytheme("spacelab"),
|
|
| 3 |
- shinyjs::useShinyjs(), |
|
| 4 |
- add_busy_spinner(spin = "double-bounce", position = "bottom-right", |
|
| 5 |
- height = "100px", width = "100px"), |
|
| 6 |
- tags$head( |
|
| 7 |
- tags$link(rel = "stylesheet", type = "text/css", href = "style.css") |
|
| 1 |
+dashboardPage( |
|
| 2 |
+ title = "GSVA Shiny Application", |
|
| 3 |
+ dashboardHeader( |
|
| 4 |
+ tags$li(class = "dropdown", |
|
| 5 |
+ tags$style(".main-header {max-height: 75px}"),
|
|
| 6 |
+ tags$style(".main-header .logo {height: 75px}"),
|
|
| 7 |
+ tags$div("GSVA Shiny Application", style = "font-size: 30px;
|
|
| 8 |
+ color: white; font-weight: bold;") |
|
| 9 |
+ ), |
|
| 10 |
+ title = tags$img(src="GSVA.png", height=75, width=75) |
|
| 8 | 11 |
), |
| 9 |
- titlePanel( |
|
| 10 |
- fluidRow(id = "title_gsva", |
|
| 11 |
- column(6, |
|
| 12 |
- h2(id="app_title", "GSVA SHINY APP", align="left")), |
|
| 13 |
- column(6, |
|
| 14 |
- h2(tags$img(src="GSVA.png", align="right", height=75, width=75))) |
|
| 15 |
- ), windowTitle="GSVA"), |
|
| 16 |
- |
|
| 17 |
- fluidRow( |
|
| 18 |
- column( |
|
| 19 |
- width=3, |
|
| 20 |
- h3("Data input"),
|
|
| 21 |
- #Select data source |
|
| 22 |
- wellPanel(fluidRow( |
|
| 23 |
- column( |
|
| 24 |
- 12, |
|
| 25 |
- matrixUI("matrix1"),
|
|
| 26 |
- fluidRow(column(12, |
|
| 27 |
- HTML("<br>"))),
|
|
| 28 |
- geneSetsUI("genes1"),
|
|
| 29 |
- HTML("<br>"),
|
|
| 30 |
- radioButtons("arg", "Change default settings:",
|
|
| 31 |
- c("No" = "no",
|
|
| 32 |
- "Yes" = "yes")), |
|
| 33 |
- actionButton("button", "Run"),
|
|
| 34 |
- fluidRow( |
|
| 35 |
- column(12, |
|
| 36 |
- HTML("<br>"),
|
|
| 37 |
- downloadUI("download"),
|
|
| 38 |
- closeBtnUI("close")
|
|
| 39 |
- ) |
|
| 40 |
- ) |
|
| 41 |
- ) |
|
| 42 |
- )) |
|
| 12 |
+ dashboardSidebar( |
|
| 13 |
+ tags$style(".left-side, .main-sidebar {padding-top: 75px}"),
|
|
| 14 |
+ tags$head( |
|
| 15 |
+ tags$link(rel = "stylesheet", type = "text/css", href = "style.css") |
|
| 43 | 16 |
), |
| 44 |
- mainPanel(width=6, |
|
| 45 |
- tabsetPanel(id = "Panels", type="tabs", |
|
| 46 |
- tabPanel("Samples",
|
|
| 47 |
- textOutput("errorsGsva"),
|
|
| 48 |
- htmlOutput("text1"),
|
|
| 49 |
- plot1_UI("plot1"),
|
|
| 50 |
- tableOutput("result")
|
|
| 51 |
- ), |
|
| 52 |
- tabPanel("GeneSets",
|
|
| 53 |
- uiOutput("text2"),
|
|
| 54 |
- htmlOutput("text3"),
|
|
| 55 |
- plot2_UI("plot2"),
|
|
| 56 |
- plot3_UI("plot3")
|
|
| 57 |
- ), |
|
| 58 |
- tabPanel("Session Info",
|
|
| 59 |
- verbatimTextOutput("sessionInfo"))
|
|
| 60 |
- ) |
|
| 17 |
+ h3("Data input"),
|
|
| 18 |
+ #Select data source |
|
| 19 |
+ matrixUI("matrix1"),
|
|
| 20 |
+ br(), |
|
| 21 |
+ geneSetsUI("genes1"),
|
|
| 22 |
+ br(), |
|
| 23 |
+ radioButtons("arg", "Change default settings:",
|
|
| 24 |
+ c("No" = "no",
|
|
| 25 |
+ "Yes" = "yes")), |
|
| 26 |
+ actionButton("button", "Run"),
|
|
| 27 |
+ br(), |
|
| 28 |
+ downloadUI("download"),
|
|
| 29 |
+ closeBtnUI("close")
|
|
| 30 |
+ ), |
|
| 31 |
+ dashboardBody( |
|
| 32 |
+ shinyjs::useShinyjs(), |
|
| 33 |
+ add_busy_spinner(spin = "double-bounce", position = "bottom-right", |
|
| 34 |
+ height = "100px", width = "100px"), |
|
| 35 |
+ box( |
|
| 36 |
+ width = 9, |
|
| 37 |
+ tabsetPanel(id = "Panels", type="tabs", |
|
| 38 |
+ tabPanel("Samples",
|
|
| 39 |
+ textOutput("errorsGsva"),
|
|
| 40 |
+ htmlOutput("text1"),
|
|
| 41 |
+ plot1_UI("plot1"),
|
|
| 42 |
+ tableOutput("result")
|
|
| 43 |
+ ), |
|
| 44 |
+ tabPanel("GeneSets",
|
|
| 45 |
+ uiOutput("text2"),
|
|
| 46 |
+ htmlOutput("text3"),
|
|
| 47 |
+ plot2_UI("plot2"),
|
|
| 48 |
+ plot3_UI("plot3")
|
|
| 49 |
+ ), |
|
| 50 |
+ tabPanel("Session Info",
|
|
| 51 |
+ verbatimTextOutput("sessionInfo"))
|
|
| 52 |
+ ) |
|
| 61 | 53 |
), |
| 62 |
- argumentsDataUI("argumentsInput")
|
|
| 54 |
+ box( |
|
| 55 |
+ width = 3, |
|
| 56 |
+ argumentsDataUI("argumentsInput")
|
|
| 57 |
+ ) |
|
| 63 | 58 |
) |
| 64 | 59 |
) |
pablo-rodr-bio2 authored on 30/04/2021 10:26:32
| ... | ... |
@@ -1,16 +1,17 @@ |
| 1 | 1 |
fluidPage( |
| 2 | 2 |
theme = shinytheme("spacelab"),
|
| 3 | 3 |
shinyjs::useShinyjs(), |
| 4 |
- add_busy_spinner(spin = "double-bounce", position = "bottom-right", height = "100px", width = "100px"), |
|
| 4 |
+ add_busy_spinner(spin = "double-bounce", position = "bottom-right", |
|
| 5 |
+ height = "100px", width = "100px"), |
|
| 5 | 6 |
tags$head( |
| 6 | 7 |
tags$link(rel = "stylesheet", type = "text/css", href = "style.css") |
| 7 | 8 |
), |
| 8 |
- titlePanel( |
|
| 9 |
- fluidRow( |
|
| 9 |
+ titlePanel( |
|
| 10 |
+ fluidRow(id = "title_gsva", |
|
| 10 | 11 |
column(6, |
| 11 |
- h2("GSVA Shiny App", align="left")),
|
|
| 12 |
+ h2(id="app_title", "GSVA SHINY APP", align="left")), |
|
| 12 | 13 |
column(6, |
| 13 |
- tags$img(src="GSVA.png", align="right", height=75, width=75)) |
|
| 14 |
+ h2(tags$img(src="GSVA.png", align="right", height=75, width=75))) |
|
| 14 | 15 |
), windowTitle="GSVA"), |
| 15 | 16 |
|
| 16 | 17 |
fluidRow( |
pablo-rodr-bio2 authored on 26/04/2021 19:22:13
| ... | ... |
@@ -29,7 +29,15 @@ fluidPage( |
| 29 | 29 |
radioButtons("arg", "Change default settings:",
|
| 30 | 30 |
c("No" = "no",
|
| 31 | 31 |
"Yes" = "yes")), |
| 32 |
- actionButton("button", "Run"))
|
|
| 32 |
+ actionButton("button", "Run"),
|
|
| 33 |
+ fluidRow( |
|
| 34 |
+ column(12, |
|
| 35 |
+ HTML("<br>"),
|
|
| 36 |
+ downloadUI("download"),
|
|
| 37 |
+ closeBtnUI("close")
|
|
| 38 |
+ ) |
|
| 39 |
+ ) |
|
| 40 |
+ ) |
|
| 33 | 41 |
)) |
| 34 | 42 |
), |
| 35 | 43 |
mainPanel(width=6, |
| ... | ... |
@@ -38,15 +46,14 @@ fluidPage( |
| 38 | 46 |
textOutput("errorsGsva"),
|
| 39 | 47 |
htmlOutput("text1"),
|
| 40 | 48 |
plot1_UI("plot1"),
|
| 41 |
- tableOutput("result"),
|
|
| 42 |
- downloadUI("download"),
|
|
| 43 |
- closeBtnUI("close")),
|
|
| 49 |
+ tableOutput("result")
|
|
| 50 |
+ ), |
|
| 44 | 51 |
tabPanel("GeneSets",
|
| 45 | 52 |
uiOutput("text2"),
|
| 46 | 53 |
htmlOutput("text3"),
|
| 47 | 54 |
plot2_UI("plot2"),
|
| 48 | 55 |
plot3_UI("plot3")
|
| 49 |
- ), |
|
| 56 |
+ ), |
|
| 50 | 57 |
tabPanel("Session Info",
|
| 51 | 58 |
verbatimTextOutput("sessionInfo"))
|
| 52 | 59 |
) |
pablo-rodr-bio2 authored on 23/04/2021 10:14:15
| ... | ... |
@@ -33,11 +33,7 @@ fluidPage( |
| 33 | 33 |
)) |
| 34 | 34 |
), |
| 35 | 35 |
mainPanel(width=6, |
| 36 |
-<<<<<<< HEAD |
|
| 37 |
- tabsetPanel(type="tabs", |
|
| 38 |
-======= |
|
| 39 | 36 |
tabsetPanel(id = "Panels", type="tabs", |
| 40 |
->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d |
|
| 41 | 37 |
tabPanel("Samples",
|
| 42 | 38 |
textOutput("errorsGsva"),
|
| 43 | 39 |
htmlOutput("text1"),
|
| ... | ... |
@@ -45,11 +41,7 @@ fluidPage( |
| 45 | 41 |
tableOutput("result"),
|
| 46 | 42 |
downloadUI("download"),
|
| 47 | 43 |
closeBtnUI("close")),
|
| 48 |
-<<<<<<< HEAD |
|
| 49 |
- tabPanel("Gene Sets",
|
|
| 50 |
-======= |
|
| 51 | 44 |
tabPanel("GeneSets",
|
| 52 |
->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d |
|
| 53 | 45 |
uiOutput("text2"),
|
| 54 | 46 |
htmlOutput("text3"),
|
| 55 | 47 |
plot2_UI("plot2"),
|
pablo-rodr-bio2 authored on 22/04/2021 22:05:25
pablo-rodr-bio2 authored on 13/04/2021 17:00:38
pablo-rodr-bio2 authored on 12/04/2021 19:45:21
| ... | ... |
@@ -51,38 +51,5 @@ fluidPage( |
| 51 | 51 |
) |
| 52 | 52 |
), |
| 53 | 53 |
argumentsDataUI("argumentsInput")
|
| 54 |
- # column( |
|
| 55 |
- # width=3, |
|
| 56 |
- # conditionalPanel( |
|
| 57 |
- # condition = "input.arg == 'yes'", |
|
| 58 |
- # h3("Parameters"),
|
|
| 59 |
- # wellPanel(fluidRow( |
|
| 60 |
- # column( |
|
| 61 |
- # 12, |
|
| 62 |
- # selectInput("method", "Choose method:",
|
|
| 63 |
- # c("gsva","ssgsea","zscore","plage")),
|
|
| 64 |
- # selectInput("kcdf", "Choose kcdf:",
|
|
| 65 |
- # c("Gaussian","Poisson","none")),
|
|
| 66 |
- # radioButtons("absRanking", "abs.ranking:",
|
|
| 67 |
- # c("False" = FALSE,
|
|
| 68 |
- # "True" = TRUE)), |
|
| 69 |
- # numericInput("minSz","min.sz:",value = 1),
|
|
| 70 |
- # numericInput("maxSz","max.sz (Write 0 for infinite):",value = 0),
|
|
| 71 |
- # radioButtons("mxDiff", "mx.diff:",
|
|
| 72 |
- # c("True" = TRUE,
|
|
| 73 |
- # "False" = FALSE)), |
|
| 74 |
- # conditionalPanel( |
|
| 75 |
- # condition = "input.method == 'gsva'", |
|
| 76 |
- # numericInput("tau1","tau:",value = 1)
|
|
| 77 |
- # ), |
|
| 78 |
- # conditionalPanel( |
|
| 79 |
- # condition = "input.method == 'ssgsea'", |
|
| 80 |
- # numericInput("tau2","tau:",value = 0.25),
|
|
| 81 |
- # radioButtons("ssgseaNorm", "ssgsea.norm:",
|
|
| 82 |
- # c("True" = TRUE,
|
|
| 83 |
- # "False" = FALSE))) |
|
| 84 |
- # ))) |
|
| 85 |
- # ) |
|
| 86 |
- # ) |
|
| 87 | 54 |
) |
| 88 | 55 |
) |
pablo-rodr-bio2 authored on 12/04/2021 19:41:34
| ... | ... |
@@ -1,147 +1,88 @@ |
| 1 |
-library(shiny) |
|
| 2 |
-library(shinythemes) |
|
| 3 |
-library(plotly) |
|
| 4 |
- |
|
| 5 |
-selectDataInput <- function(id) {
|
|
| 6 |
- # Create a namespace function using the provided id |
|
| 7 |
- ns <- NS(id) |
|
| 8 |
- |
|
| 9 |
- #UI declaration |
|
| 10 |
- column( |
|
| 11 |
- 3, |
|
| 12 |
- h3("Data input:"),
|
|
| 13 |
- #Select data source |
|
| 14 |
- wellPanel(fluidRow( |
|
| 15 |
- column( |
|
| 16 |
- 12, |
|
| 17 |
- #Select expression data matrix |
|
| 18 |
- radioButtons("matrixSourceType", "Select expression data matrix:",
|
|
| 19 |
- c("From file" = "fileMatrix",
|
|
| 20 |
- "From workspace" = "varMatrix")) |
|
| 21 |
- , |
|
| 22 |
- #If the selected data source is a file |
|
| 23 |
- conditionalPanel( |
|
| 24 |
- condition = "input.matrixSourceType == 'fileMatrix'", |
|
| 25 |
- fileInput("matrixFile", "Choose matrix file:",
|
|
| 26 |
- accept = c( |
|
| 27 |
- "text/csv", |
|
| 28 |
- "text/comma-separated-values,text/plain", |
|
| 29 |
- ".csv",".ods",".xls",".xlt") |
|
| 30 |
- ) |
|
| 31 |
- ), |
|
| 32 |
- #If the selected data source is a workspace object |
|
| 33 |
- conditionalPanel( |
|
| 34 |
- condition = "input.matrixSourceType == 'varMatrix'", |
|
| 35 |
- selectInput("matrixVar", "Choose matrix var:",
|
|
| 36 |
- ls(envir=.GlobalEnv)) |
|
| 37 |
- ), |
|
| 38 |
- fluidRow(column(12, |
|
| 39 |
- HTML("<br>"))),
|
|
| 40 |
- #Select geneset |
|
| 41 |
- radioButtons("genesetSourceType", "Select gene sets:",
|
|
| 42 |
- c("From file" = "fileGeneset",
|
|
| 43 |
- "From workspace" = "varGeneset")) |
|
| 44 |
- , |
|
| 45 |
- #If the selected data source is a file |
|
| 46 |
- conditionalPanel( |
|
| 47 |
- condition = "input.genesetSourceType == 'fileGeneset'", |
|
| 48 |
- fileInput("genesetFile", "Choose GeneSet file:",
|
|
| 49 |
- accept = ".gmt") |
|
| 50 |
- ), |
|
| 51 |
- #If the selected data source is a workspace object |
|
| 52 |
- conditionalPanel( |
|
| 53 |
- condition = "input.genesetSourceType == 'varGeneset'", |
|
| 54 |
- selectInput("genesetVar", "Choose GeneSet var:",
|
|
| 55 |
- ls(envir=.GlobalEnv)) |
|
| 56 |
- ), |
|
| 57 |
- HTML("<br>"),
|
|
| 58 |
- radioButtons("arg", "Change default settings:",
|
|
| 59 |
- c("No" = "no",
|
|
| 60 |
- "Yes" = "yes")) |
|
| 61 |
- ) |
|
| 62 |
- ), |
|
| 63 |
- actionButton("button", "Run"))
|
|
| 64 |
- ) |
|
| 65 |
-} |
|
| 66 |
- |
|
| 67 |
-mainDataInput <- function(id) {
|
|
| 68 |
- # Create a namespace function using the provided id |
|
| 69 |
- ns <- NS(id) |
|
| 70 |
- |
|
| 71 |
- #UI Definition |
|
| 72 |
- mainPanel( width = 6, |
|
| 73 |
- tabsetPanel(type="tabs", |
|
| 74 |
- tabPanel("Samples",
|
|
| 75 |
- htmlOutput("text1"),
|
|
| 76 |
- plotlyOutput("plot"),
|
|
| 77 |
- tableOutput("result"),
|
|
| 78 |
- uiOutput("download")),
|
|
| 79 |
- tabPanel("Gene Sets",
|
|
| 80 |
- uiOutput("text2"),
|
|
| 81 |
- htmlOutput("text3"),
|
|
| 82 |
- plotlyOutput("plot2"),
|
|
| 83 |
- plotlyOutput("plot3")),
|
|
| 84 |
- tabPanel("Session Info",
|
|
| 85 |
- verbatimTextOutput("sessionInfo"))
|
|
| 86 |
- ) |
|
| 87 |
- ) |
|
| 88 |
-} |
|
| 89 |
- |
|
| 90 |
-argumentsDataInput <- function(id) {
|
|
| 91 |
- # Create a namespace function using the provided id |
|
| 92 |
- ns <- NS(id) |
|
| 1 |
+fluidPage( |
|
| 2 |
+ theme = shinytheme("spacelab"),
|
|
| 3 |
+ shinyjs::useShinyjs(), |
|
| 4 |
+ add_busy_spinner(spin = "double-bounce", position = "bottom-right", height = "100px", width = "100px"), |
|
| 5 |
+ tags$head( |
|
| 6 |
+ tags$link(rel = "stylesheet", type = "text/css", href = "style.css") |
|
| 7 |
+ ), |
|
| 8 |
+ titlePanel( |
|
| 9 |
+ fluidRow( |
|
| 10 |
+ column(6, |
|
| 11 |
+ h2("GSVA Shiny App", align="left")),
|
|
| 12 |
+ column(6, |
|
| 13 |
+ tags$img(src="GSVA.png", align="right", height=75, width=75)) |
|
| 14 |
+ ), windowTitle="GSVA"), |
|
| 93 | 15 |
|
| 94 |
- #UI Definition |
|
| 95 |
- column( |
|
| 96 |
- 3, |
|
| 97 |
- conditionalPanel( |
|
| 98 |
- condition = "input.arg == 'yes'", |
|
| 99 |
- h3("Parameters:"),
|
|
| 16 |
+ fluidRow( |
|
| 17 |
+ column( |
|
| 18 |
+ width=3, |
|
| 19 |
+ h3("Data input"),
|
|
| 20 |
+ #Select data source |
|
| 100 | 21 |
wellPanel(fluidRow( |
| 101 | 22 |
column( |
| 102 | 23 |
12, |
| 103 |
- selectInput("method", "Choose method:",
|
|
| 104 |
- c("gsva","ssgsea","zscore","plage")),
|
|
| 105 |
- selectInput("kcdf", "Choose kcdf:",
|
|
| 106 |
- c("Gaussian","Poisson","none")),
|
|
| 107 |
- radioButtons("absRanking", "abs.ranking:",
|
|
| 108 |
- c("False" = FALSE,
|
|
| 109 |
- "True" = TRUE)), |
|
| 110 |
- numericInput("minSz","min.sz:",value = 1),
|
|
| 111 |
- numericInput("maxSz","max.sz (Write 0 for infinite):",value = 0),
|
|
| 112 |
- radioButtons("mxDiff", "mx.diff:",
|
|
| 113 |
- c("True" = TRUE,
|
|
| 114 |
- "False" = FALSE)), |
|
| 115 |
- conditionalPanel( |
|
| 116 |
- condition = "input.method == 'gsva'", |
|
| 117 |
- numericInput("tau1","tau:",value = 1)
|
|
| 118 |
- ), |
|
| 119 |
- conditionalPanel( |
|
| 120 |
- condition = "input.method == 'ssgsea'", |
|
| 121 |
- numericInput("tau2","tau:",value = 0.25),
|
|
| 122 |
- radioButtons("ssgseaNorm", "ssgsea.norm:",
|
|
| 123 |
- c("True" = TRUE,
|
|
| 124 |
- "False" = FALSE)), |
|
| 125 |
- ), |
|
| 126 |
- radioButtons("verbose", "verbose:",
|
|
| 127 |
- c("True" = TRUE,
|
|
| 128 |
- "False" = FALSE)) |
|
| 129 |
- ))) |
|
| 130 |
- ) |
|
| 24 |
+ matrixUI("matrix1"),
|
|
| 25 |
+ fluidRow(column(12, |
|
| 26 |
+ HTML("<br>"))),
|
|
| 27 |
+ geneSetsUI("genes1"),
|
|
| 28 |
+ HTML("<br>"),
|
|
| 29 |
+ radioButtons("arg", "Change default settings:",
|
|
| 30 |
+ c("No" = "no",
|
|
| 31 |
+ "Yes" = "yes")), |
|
| 32 |
+ actionButton("button", "Run"))
|
|
| 33 |
+ )) |
|
| 34 |
+ ), |
|
| 35 |
+ mainPanel(width=6, |
|
| 36 |
+ tabsetPanel(type="tabs", |
|
| 37 |
+ tabPanel("Samples",
|
|
| 38 |
+ textOutput("errorsGsva"),
|
|
| 39 |
+ htmlOutput("text1"),
|
|
| 40 |
+ plot1_UI("plot1"),
|
|
| 41 |
+ tableOutput("result"),
|
|
| 42 |
+ downloadUI("download")),
|
|
| 43 |
+ tabPanel("Gene Sets",
|
|
| 44 |
+ uiOutput("text2"),
|
|
| 45 |
+ htmlOutput("text3"),
|
|
| 46 |
+ plot2_UI("plot2"),
|
|
| 47 |
+ plot3_UI("plot3")
|
|
| 48 |
+ ), |
|
| 49 |
+ tabPanel("Session Info",
|
|
| 50 |
+ verbatimTextOutput("sessionInfo"))
|
|
| 51 |
+ ) |
|
| 52 |
+ ), |
|
| 53 |
+ argumentsDataUI("argumentsInput")
|
|
| 54 |
+ # column( |
|
| 55 |
+ # width=3, |
|
| 56 |
+ # conditionalPanel( |
|
| 57 |
+ # condition = "input.arg == 'yes'", |
|
| 58 |
+ # h3("Parameters"),
|
|
| 59 |
+ # wellPanel(fluidRow( |
|
| 60 |
+ # column( |
|
| 61 |
+ # 12, |
|
| 62 |
+ # selectInput("method", "Choose method:",
|
|
| 63 |
+ # c("gsva","ssgsea","zscore","plage")),
|
|
| 64 |
+ # selectInput("kcdf", "Choose kcdf:",
|
|
| 65 |
+ # c("Gaussian","Poisson","none")),
|
|
| 66 |
+ # radioButtons("absRanking", "abs.ranking:",
|
|
| 67 |
+ # c("False" = FALSE,
|
|
| 68 |
+ # "True" = TRUE)), |
|
| 69 |
+ # numericInput("minSz","min.sz:",value = 1),
|
|
| 70 |
+ # numericInput("maxSz","max.sz (Write 0 for infinite):",value = 0),
|
|
| 71 |
+ # radioButtons("mxDiff", "mx.diff:",
|
|
| 72 |
+ # c("True" = TRUE,
|
|
| 73 |
+ # "False" = FALSE)), |
|
| 74 |
+ # conditionalPanel( |
|
| 75 |
+ # condition = "input.method == 'gsva'", |
|
| 76 |
+ # numericInput("tau1","tau:",value = 1)
|
|
| 77 |
+ # ), |
|
| 78 |
+ # conditionalPanel( |
|
| 79 |
+ # condition = "input.method == 'ssgsea'", |
|
| 80 |
+ # numericInput("tau2","tau:",value = 0.25),
|
|
| 81 |
+ # radioButtons("ssgseaNorm", "ssgsea.norm:",
|
|
| 82 |
+ # c("True" = TRUE,
|
|
| 83 |
+ # "False" = FALSE))) |
|
| 84 |
+ # ))) |
|
| 85 |
+ # ) |
|
| 86 |
+ # ) |
|
| 131 | 87 |
) |
| 132 |
-} |
|
| 133 |
- |
|
| 134 |
-fluidPage( |
|
| 135 |
- theme = shinytheme("spacelab"),
|
|
| 136 |
- tags$head( |
|
| 137 |
- tags$link(rel = "stylesheet", type = "text/css", href = "style.css") |
|
| 138 |
- ), |
|
| 139 |
- titlePanel(div(h2("GSVA WebApp", align="left"),
|
|
| 140 |
- tags$img(src="GSVA.png", align="center", height=75, width=75)), |
|
| 141 |
- windowTitle="GSVA"), |
|
| 142 |
- fluidRow( |
|
| 143 |
- selectDataInput("dataInput"),
|
|
| 144 |
- mainDataInput("mainInput"),
|
|
| 145 |
- argumentsDataInput("argumentsInput")
|
|
| 146 |
- ) |
|
| 147 | 88 |
) |
pablo-rodr-bio2 authored on 21/04/2021 10:51:28
| ... | ... |
@@ -33,7 +33,7 @@ fluidPage( |
| 33 | 33 |
)) |
| 34 | 34 |
), |
| 35 | 35 |
mainPanel(width=6, |
| 36 |
- tabsetPanel(type="tabs", |
|
| 36 |
+ tabsetPanel(id = "Panels", type="tabs", |
|
| 37 | 37 |
tabPanel("Samples",
|
| 38 | 38 |
textOutput("errorsGsva"),
|
| 39 | 39 |
htmlOutput("text1"),
|
| ... | ... |
@@ -41,7 +41,7 @@ fluidPage( |
| 41 | 41 |
tableOutput("result"),
|
| 42 | 42 |
downloadUI("download"),
|
| 43 | 43 |
closeBtnUI("close")),
|
| 44 |
- tabPanel("Gene Sets",
|
|
| 44 |
+ tabPanel("GeneSets",
|
|
| 45 | 45 |
uiOutput("text2"),
|
| 46 | 46 |
htmlOutput("text3"),
|
| 47 | 47 |
plot2_UI("plot2"),
|
pablo-rodr-bio2 authored on 13/04/2021 17:00:38
pablo-rodr-bio2 authored on 12/04/2021 19:45:21
| ... | ... |
@@ -51,38 +51,5 @@ fluidPage( |
| 51 | 51 |
) |
| 52 | 52 |
), |
| 53 | 53 |
argumentsDataUI("argumentsInput")
|
| 54 |
- # column( |
|
| 55 |
- # width=3, |
|
| 56 |
- # conditionalPanel( |
|
| 57 |
- # condition = "input.arg == 'yes'", |
|
| 58 |
- # h3("Parameters"),
|
|
| 59 |
- # wellPanel(fluidRow( |
|
| 60 |
- # column( |
|
| 61 |
- # 12, |
|
| 62 |
- # selectInput("method", "Choose method:",
|
|
| 63 |
- # c("gsva","ssgsea","zscore","plage")),
|
|
| 64 |
- # selectInput("kcdf", "Choose kcdf:",
|
|
| 65 |
- # c("Gaussian","Poisson","none")),
|
|
| 66 |
- # radioButtons("absRanking", "abs.ranking:",
|
|
| 67 |
- # c("False" = FALSE,
|
|
| 68 |
- # "True" = TRUE)), |
|
| 69 |
- # numericInput("minSz","min.sz:",value = 1),
|
|
| 70 |
- # numericInput("maxSz","max.sz (Write 0 for infinite):",value = 0),
|
|
| 71 |
- # radioButtons("mxDiff", "mx.diff:",
|
|
| 72 |
- # c("True" = TRUE,
|
|
| 73 |
- # "False" = FALSE)), |
|
| 74 |
- # conditionalPanel( |
|
| 75 |
- # condition = "input.method == 'gsva'", |
|
| 76 |
- # numericInput("tau1","tau:",value = 1)
|
|
| 77 |
- # ), |
|
| 78 |
- # conditionalPanel( |
|
| 79 |
- # condition = "input.method == 'ssgsea'", |
|
| 80 |
- # numericInput("tau2","tau:",value = 0.25),
|
|
| 81 |
- # radioButtons("ssgseaNorm", "ssgsea.norm:",
|
|
| 82 |
- # c("True" = TRUE,
|
|
| 83 |
- # "False" = FALSE))) |
|
| 84 |
- # ))) |
|
| 85 |
- # ) |
|
| 86 |
- # ) |
|
| 87 | 54 |
) |
| 88 | 55 |
) |
pablo-rodr-bio2 authored on 12/04/2021 19:41:34
| ... | ... |
@@ -1,147 +1,88 @@ |
| 1 |
-library(shiny) |
|
| 2 |
-library(shinythemes) |
|
| 3 |
-library(plotly) |
|
| 4 |
- |
|
| 5 |
-selectDataInput <- function(id) {
|
|
| 6 |
- # Create a namespace function using the provided id |
|
| 7 |
- ns <- NS(id) |
|
| 8 |
- |
|
| 9 |
- #UI declaration |
|
| 10 |
- column( |
|
| 11 |
- 3, |
|
| 12 |
- h3("Data input:"),
|
|
| 13 |
- #Select data source |
|
| 14 |
- wellPanel(fluidRow( |
|
| 15 |
- column( |
|
| 16 |
- 12, |
|
| 17 |
- #Select expression data matrix |
|
| 18 |
- radioButtons("matrixSourceType", "Select expression data matrix:",
|
|
| 19 |
- c("From file" = "fileMatrix",
|
|
| 20 |
- "From workspace" = "varMatrix")) |
|
| 21 |
- , |
|
| 22 |
- #If the selected data source is a file |
|
| 23 |
- conditionalPanel( |
|
| 24 |
- condition = "input.matrixSourceType == 'fileMatrix'", |
|
| 25 |
- fileInput("matrixFile", "Choose matrix file:",
|
|
| 26 |
- accept = c( |
|
| 27 |
- "text/csv", |
|
| 28 |
- "text/comma-separated-values,text/plain", |
|
| 29 |
- ".csv",".ods",".xls",".xlt") |
|
| 30 |
- ) |
|
| 31 |
- ), |
|
| 32 |
- #If the selected data source is a workspace object |
|
| 33 |
- conditionalPanel( |
|
| 34 |
- condition = "input.matrixSourceType == 'varMatrix'", |
|
| 35 |
- selectInput("matrixVar", "Choose matrix var:",
|
|
| 36 |
- ls(envir=.GlobalEnv)) |
|
| 37 |
- ), |
|
| 38 |
- fluidRow(column(12, |
|
| 39 |
- HTML("<br>"))),
|
|
| 40 |
- #Select geneset |
|
| 41 |
- radioButtons("genesetSourceType", "Select gene sets:",
|
|
| 42 |
- c("From file" = "fileGeneset",
|
|
| 43 |
- "From workspace" = "varGeneset")) |
|
| 44 |
- , |
|
| 45 |
- #If the selected data source is a file |
|
| 46 |
- conditionalPanel( |
|
| 47 |
- condition = "input.genesetSourceType == 'fileGeneset'", |
|
| 48 |
- fileInput("genesetFile", "Choose GeneSet file:",
|
|
| 49 |
- accept = ".gmt") |
|
| 50 |
- ), |
|
| 51 |
- #If the selected data source is a workspace object |
|
| 52 |
- conditionalPanel( |
|
| 53 |
- condition = "input.genesetSourceType == 'varGeneset'", |
|
| 54 |
- selectInput("genesetVar", "Choose GeneSet var:",
|
|
| 55 |
- ls(envir=.GlobalEnv)) |
|
| 56 |
- ), |
|
| 57 |
- HTML("<br>"),
|
|
| 58 |
- radioButtons("arg", "Change default settings:",
|
|
| 59 |
- c("No" = "no",
|
|
| 60 |
- "Yes" = "yes")) |
|
| 61 |
- ) |
|
| 62 |
- ), |
|
| 63 |
- actionButton("button", "Run"))
|
|
| 64 |
- ) |
|
| 65 |
-} |
|
| 66 |
- |
|
| 67 |
-mainDataInput <- function(id) {
|
|
| 68 |
- # Create a namespace function using the provided id |
|
| 69 |
- ns <- NS(id) |
|
| 70 |
- |
|
| 71 |
- #UI Definition |
|
| 72 |
- mainPanel( width = 6, |
|
| 73 |
- tabsetPanel(type="tabs", |
|
| 74 |
- tabPanel("Samples",
|
|
| 75 |
- htmlOutput("text1"),
|
|
| 76 |
- plotlyOutput("plot"),
|
|
| 77 |
- tableOutput("result"),
|
|
| 78 |
- uiOutput("download")),
|
|
| 79 |
- tabPanel("Gene Sets",
|
|
| 80 |
- uiOutput("text2"),
|
|
| 81 |
- htmlOutput("text3"),
|
|
| 82 |
- plotlyOutput("plot2"),
|
|
| 83 |
- plotlyOutput("plot3")),
|
|
| 84 |
- tabPanel("Session Info",
|
|
| 85 |
- verbatimTextOutput("sessionInfo"))
|
|
| 86 |
- ) |
|
| 87 |
- ) |
|
| 88 |
-} |
|
| 89 |
- |
|
| 90 |
-argumentsDataInput <- function(id) {
|
|
| 91 |
- # Create a namespace function using the provided id |
|
| 92 |
- ns <- NS(id) |
|
| 1 |
+fluidPage( |
|
| 2 |
+ theme = shinytheme("spacelab"),
|
|
| 3 |
+ shinyjs::useShinyjs(), |
|
| 4 |
+ add_busy_spinner(spin = "double-bounce", position = "bottom-right", height = "100px", width = "100px"), |
|
| 5 |
+ tags$head( |
|
| 6 |
+ tags$link(rel = "stylesheet", type = "text/css", href = "style.css") |
|
| 7 |
+ ), |
|
| 8 |
+ titlePanel( |
|
| 9 |
+ fluidRow( |
|
| 10 |
+ column(6, |
|
| 11 |
+ h2("GSVA Shiny App", align="left")),
|
|
| 12 |
+ column(6, |
|
| 13 |
+ tags$img(src="GSVA.png", align="right", height=75, width=75)) |
|
| 14 |
+ ), windowTitle="GSVA"), |
|
| 93 | 15 |
|
| 94 |
- #UI Definition |
|
| 95 |
- column( |
|
| 96 |
- 3, |
|
| 97 |
- conditionalPanel( |
|
| 98 |
- condition = "input.arg == 'yes'", |
|
| 99 |
- h3("Parameters:"),
|
|
| 16 |
+ fluidRow( |
|
| 17 |
+ column( |
|
| 18 |
+ width=3, |
|
| 19 |
+ h3("Data input"),
|
|
| 20 |
+ #Select data source |
|
| 100 | 21 |
wellPanel(fluidRow( |
| 101 | 22 |
column( |
| 102 | 23 |
12, |
| 103 |
- selectInput("method", "Choose method:",
|
|
| 104 |
- c("gsva","ssgsea","zscore","plage")),
|
|
| 105 |
- selectInput("kcdf", "Choose kcdf:",
|
|
| 106 |
- c("Gaussian","Poisson","none")),
|
|
| 107 |
- radioButtons("absRanking", "abs.ranking:",
|
|
| 108 |
- c("False" = FALSE,
|
|
| 109 |
- "True" = TRUE)), |
|
| 110 |
- numericInput("minSz","min.sz:",value = 1),
|
|
| 111 |
- numericInput("maxSz","max.sz (Write 0 for infinite):",value = 0),
|
|
| 112 |
- radioButtons("mxDiff", "mx.diff:",
|
|
| 113 |
- c("True" = TRUE,
|
|
| 114 |
- "False" = FALSE)), |
|
| 115 |
- conditionalPanel( |
|
| 116 |
- condition = "input.method == 'gsva'", |
|
| 117 |
- numericInput("tau1","tau:",value = 1)
|
|
| 118 |
- ), |
|
| 119 |
- conditionalPanel( |
|
| 120 |
- condition = "input.method == 'ssgsea'", |
|
| 121 |
- numericInput("tau2","tau:",value = 0.25),
|
|
| 122 |
- radioButtons("ssgseaNorm", "ssgsea.norm:",
|
|
| 123 |
- c("True" = TRUE,
|
|
| 124 |
- "False" = FALSE)), |
|
| 125 |