inst/ui.r
In decusInLabore/biologicSC: What the Package Does (One Line, Title Case)
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dfkey <- read.delim("connect/db.txt", header = T, sep="\t", stringsAsFactors = F)
library(shiny)
library(ggplot2)
library(yaml)
pos <- grep("type", names(dfkey))
if (length(pos) > 0 & dfkey$type == "RSQLite"){
library(RSQLite)
mode = "SQLite"
} else {
library(RMySQL)
host <- as.character(dfkey$url)
user <- as.character(dfkey$id)
DBpd <- as.character(dfkey$id2)
mode = "SQL"
}
library(DT)
geneDefault = as.character(dfkey$default)
dbname <- as.character(dfkey$db)
coordinateTbName <- as.character(dfkey$coordTb)
exprTbName <- as.character(dfkey$exprTb)
geneID_TbName <- as.character(dfkey$geneTb)
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oldw <- getOption("warn")
options(warn = -1)
if (mode == "SQLite"){
setwd("data")
dbDB <- dbConnect(RSQLite::SQLite(), dbname=dbname)
setwd("..")
} else {
dbDB <- dbConnect(MySQL(), user = user, password = DBpd, host = host, dbname=dbname)
}
query <- paste0("SELECT DISTINCT * FROM ", coordinateTbName)
dfCoordSel <- dbGetQuery(dbDB, query)
dbDisconnect(dbDB)
dfCoordSel[["all"]] <- "all"
## ##
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## Get XYsel from yaml if possible ##
if (file.exists("parameters/parameters.yaml")){
Yparams <- yaml.load(
read_yaml(
"parameters/parameters.yaml",
fileEncoding = "UTF-8"
))
## Check ##
checkVec <- c(
names(dfCoordSel)
)
params <- list(
"XYsel" = unique(Yparams[["XYsel"]][Yparams[["XYsel"]] %in% checkVec]),
"allColorOptions" = unique(Yparams[["allColorOptions"]][Yparams[["allColorOptions"]] %in% checkVec]),
"splitOptions" = unique(Yparams[["splitOptions"]][Yparams[["splitOptions"]] %in% checkVec]),
"sampleColorList" = unique(Yparams[["sampleColorList"]][Yparams[["sampleColorList"]] %in% checkVec])
)
names(params[["XYsel"]]) <- unique(Yparams[["XYsel_names"]][Yparams[["XYsel"]] %in% checkVec])
names(params[["allColorOptions"]]) <- Yparams[["allColorOptions_names"]][Yparams[["allColorOptions"]] %in% checkVec]
names(params[["splitOptions"]]) <- Yparams[["splitOptions_names"]][Yparams[["splitOptions"]] %in% checkVec]
names(params[["sampleColorList"]]) <- Yparams[["sampleColorList_names"]][Yparams[["sampleColorList"]] %in% checkVec]
} else {
params <- list(
"XYsel" = c(
names(dfCoordSel)[grep("UMAP", names(dfCoordSel))],
names(dfCoordSel)[grep("tSNE", names(dfCoordSel))],
names(dfCoordSel)[grep("seurat_clusters", names(dfCoordSel))],
names(dfCoordSel)[grep("sub_clusters", names(dfCoordSel))],
names(dfCoordSel)[grep("PC", names(dfCoordSel))],
names(dfCoordSel)[grep("DM_Pseudotime", names(dfCoordSel))],
names(dfCoordSel)[grep("DF_Classification", names(dfCoordSel))],
names(dfCoordSel)[grep("nCount", names(dfCoordSel))],
names(dfCoordSel)[grep("nFeatures", names(dfCoordSel))],
names(dfCoordSel)[grep("percent", names(dfCoordSel))],
names(dfCoordSel)[grep("Con_Prad_AZ", names(dfCoordSel))],
names(dfCoordSel)[grep("Norm_Hyp", names(dfCoordSel))],
names(dfCoordSel)[grep("Gender", names(dfCoordSel))],
names(dfCoordSel)[grep("CellFromTumor", names(dfCoordSel))],
names(dfCoordSel)[grep("Patient", names(dfCoordSel))],
names(dfCoordSel)[grep("Region", names(dfCoordSel))],
names(dfCoordSel)[grep("Article_Cell_Type", names(dfCoordSel))]
),
"allColorOptions" = c(
#"Log10 Expresson" = "lg10Expr",
"DM Pseudotime" = names(dfCoordSel)[grep("DM_Pseudotime", names(dfCoordSel))],
"SampleID" = names(dfCoordSel)[grep("sampleID", names(dfCoordSel))],
"Gender" = names(dfCoordSel)[grep("Gender", names(dfCoordSel))],
"Patient" = names(dfCoordSel)[grep("Patient", names(dfCoordSel))],
"Doublet Classification" = names(dfCoordSel)[grep("DF_Classification", names(dfCoordSel))] ,
"Cluster" = names(dfCoordSel)[grep("seurat_clusters", names(dfCoordSel))] ,
"nCount_RNA" = names(dfCoordSel)[grep("nCount_RNA", names(dfCoordSel))],
"nFeature_RNA" = names(dfCoordSel)[grep("nFeature_RNA", names(dfCoordSel))],
"percent_mt" = names(dfCoordSel)[grep("percent_mt", names(dfCoordSel))],
"S Phase Score" = names(dfCoordSel)[grep("S_Score", names(dfCoordSel))],
"G2M Score" = names(dfCoordSel)[grep("G2M_Score", names(dfCoordSel))],
"Cell Cycle Phase" = names(dfCoordSel)[grep("Phase", names(dfCoordSel))],
"Uniform" = names(dfCoordSel)[grep("all", names(dfCoordSel))]
),
"splitOptions" = c(
#"Log10 Expresson" = "lg10Expr",
"DM Pseudotime" = names(dfCoordSel)[grep("DM_Pseudotime", names(dfCoordSel))],
"SampleID" = names(dfCoordSel)[grep("sampleID", names(dfCoordSel))],
"Gender" = names(dfCoordSel)[grep("Gender", names(dfCoordSel))],
"Patient" = names(dfCoordSel)[grep("Patient", names(dfCoordSel))],
"Doublet Classification" = names(dfCoordSel)[grep("DF_Classification", names(dfCoordSel))] ,
"Cluster" = names(dfCoordSel)[grep("seurat_clusters", names(dfCoordSel))] ,
"nCount_RNA" = names(dfCoordSel)[grep("nCount_RNA", names(dfCoordSel))],
"nFeature_RNA" = names(dfCoordSel)[grep("nFeature_RNA", names(dfCoordSel))],
"percent_mt" = names(dfCoordSel)[grep("percent_mt", names(dfCoordSel))],
"S Phase Score" = names(dfCoordSel)[grep("S_Score", names(dfCoordSel))],
"G2M Score" = names(dfCoordSel)[grep("G2M_Score", names(dfCoordSel))],
"Cell Cycle Phase" = names(dfCoordSel)[grep("Phase", names(dfCoordSel))],
"Uniform" = names(dfCoordSel)[grep("all", names(dfCoordSel))]
)
)
}
print(params)
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Xchoices <- c("Log10 Expression" = "lg10Expr",
params[["allColorOptions"]],
params[["XYsel"]]
)
if (length(grep("^UMAP_1$", Xchoices)) == 1){
Xsel <- as.vector(Xchoices[grep("^UMAP_1$", Xchoices)])
} else {
Xsel <- as.vector(Xchoices[1])
}
Ychoices <- c("Log10 Expression" = "lg10Expr",
params[["XYsel"]]
)
if (length(grep("^UMAP_2$", Ychoices)) == 1){
Ysel <- as.vector(Ychoices[grep("^UMAP_2$", Ychoices)])
} else {
Ysel <- as.vector(Ychoices[2])
}
splitChoices <- params[["splitOptions"]]
if (length(grep("sampleID", splitChoices)) == 1){
splitSel <- as.vector(splitChoices[grep("sampleID", splitChoices)])
} else {
splitSel <- as.vector(splitChoices[1])
}
colorChoices <- c("Log10 Expression" = "lg10Expr",
params[["allColorOptions"]]
)
if (length(grep("^lg10Expr$", colorChoices)) == 1){
colSel <- as.vector(colorChoices[grep("^lg10Expr$", colorChoices)])
} else {
colSel <- as.vector(colorChoices[1])
}
spectralCols <- c(
Darkred = "#D53E4F",
Red = "#F46D43",
Orange = "#FDAE61" ,
Lightorange = "#FEE08B",
Yellow = "#FFFFBF",
Lightgreen = "#E6F598",
Green = "#ABDDA4",
Darkgreen = "#66C2A5",
Blue = "#3288BD"
)
conditionVec <- unique(sort(dfCoordSel$sampleID))
Nsamples <- length(conditionVec)
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oldw <- getOption("wafrn")
options(warn = -1)
if (mode == "SQLite"){
setwd("data")
dbDB <- dbConnect(RSQLite::SQLite(), dbname=dbname)
setwd("..")
} else {
dbDB <- dbConnect(MySQL(), user = user, password = DBpd, host = host, dbname=dbname)
}
query <- paste0("SELECT DISTINCT gene FROM ", geneID_TbName)
allGenes <- as.vector(dbGetQuery(dbDB, query)[,"gene"])
dbDisconnect(dbDB)
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shinyUI(fluidPage(
navbarPage(
"bioLOGIC SC",
tabPanel("FeatureView"),
tags$head(
tags$style(type = 'text/css',
HTML('.navbar { background-color: #42972050;}
.navbar-default .navbar-brand{color: white;}
.tab-panel{ background-color: red; color: white}
.navbar-default .navbar-nav > .active > a,
.navbar-default .navbar-nav > .active > a:focus,
.navbar-default .navbar-nav > .active > a:hover {
color: #555;
background-color: #42972050;
}')
),
tags$script(HTML("var header = $('.navbar > .container-fluid');
header.append('<div style=\"float:left\"><ahref=\"URL\"><img src=\"assets/images/logo.ico\" alt=\"alt\" style=\"float:right;width:33px;height:41px;padding-top:10px;\"> </a>`</div>');
console.log(header)")
),
tags$link(rel="shortcut icon", href="assets/images/logo.ico")
)
),
#titlePanel("FeatureView"),
sidebarLayout(
sidebarPanel(
tags$style(".well {background-color:#42972050;}"),
helpText("To create a Violin-stype Plot, select for example seurat_clusters as x-axis, lg10Expr as y-Axis and seurat_clusters as colorBy option."),
selectizeInput("gene",
label = "Gene or Category Selection",
choices = NULL, #c(as.vector(sort(unique(allGenes)))),
selected = geneDefault,
options = list(maxOptions = 50)) ,
selectInput("x_axis",
label = "Choose an X-axis",
choices = Xchoices,
selected = Xsel),
selectInput("y_axis",
label = "Choose an Y-axis",
choices =Ychoices,
selected = Ysel),
selectInput("splitByColumn",
label = "Split Plots By",
choices = splitChoices,
selected = splitSel),
selectInput("colorBy",
label = "Color Plots By",
choices = colorChoices,
selected = colSel),
selectInput("dotcolor",
label = "Choose dot colorscale",
choices =c("Darkblue" = "darkblue", spectralCols),
selected = "darkblue"),
selectInput("lowColor",
label = "Choose low colorscale",
choices =c("Grey" = "#D3D3D3", "White" = "white", spectralCols),
selected = "#D3D3D3"),
selectInput("background",
label = "Select Background",
choices =c("Grey" = "grey", "White" = "white","Minimal" = "minimal", "Plain" = "plain"),
selected = "white"),
radioButtons("dotsize", label = "Choose a Dotsize", choices = c("0.1","0.5","1","2"), selected = "1",
inline = FALSE, width = NULL, choiceNames = c("0.1","0.5","1","2"),
choiceValues = c("0.1","0.5","1","2")),
# selectInput("dotsize",
# label = "Choose an Dotsize",
# choices =c("0.1","0.5","1","2"),
# selected = "1"),
#downloadButton('downloadPlot', "Download Plot"),
#downloadButton("downloadData", "Download Data"),
# checkboxGroupInput("selected_sample",
# label = "Select Column",
# choices = seq_along(mtcars))
),
mainPanel(
fluidRow(
column(12,
uiOutput("multi_plot_ui")
)
),
fluidRow(
column(12,
textOutput("dev_text")
)
)
)
)
))
## ##
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decusInLabore/biologicSC documentation built on May 24, 2021, 4:11 p.m.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
###############################################################################
## ##
## ##
###############################################################################
###############################################################################
## ##
dfkey <- read.delim("connect/db.txt", header = T, sep="\t", stringsAsFactors = F)
library(shiny)
library(ggplot2)
library(yaml)
pos <- grep("type", names(dfkey))
if (length(pos) > 0 & dfkey$type == "RSQLite"){
library(RSQLite)
mode = "SQLite"
} else {
library(RMySQL)
host <- as.character(dfkey$url)
user <- as.character(dfkey$id)
DBpd <- as.character(dfkey$id2)
mode = "SQL"
}
library(DT)
geneDefault = as.character(dfkey$default)
dbname <- as.character(dfkey$db)
coordinateTbName <- as.character(dfkey$coordTb)
exprTbName <- as.character(dfkey$exprTb)
geneID_TbName <- as.character(dfkey$geneTb)
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oldw <- getOption("warn")
options(warn = -1)
if (mode == "SQLite"){
setwd("data")
dbDB <- dbConnect(RSQLite::SQLite(), dbname=dbname)
setwd("..")
} else {
dbDB <- dbConnect(MySQL(), user = user, password = DBpd, host = host, dbname=dbname)
}
query <- paste0("SELECT DISTINCT * FROM ", coordinateTbName)
dfCoordSel <- dbGetQuery(dbDB, query)
dbDisconnect(dbDB)
dfCoordSel[["all"]] <- "all"
## ##
###############################################################################
###############################################################################
## Get XYsel from yaml if possible ##
if (file.exists("parameters/parameters.yaml")){
Yparams <- yaml.load(
read_yaml(
"parameters/parameters.yaml",
fileEncoding = "UTF-8"
))
## Check ##
checkVec <- c(
names(dfCoordSel)
)
params <- list(
"XYsel" = unique(Yparams[["XYsel"]][Yparams[["XYsel"]] %in% checkVec]),
"allColorOptions" = unique(Yparams[["allColorOptions"]][Yparams[["allColorOptions"]] %in% checkVec]),
"splitOptions" = unique(Yparams[["splitOptions"]][Yparams[["splitOptions"]] %in% checkVec]),
"sampleColorList" = unique(Yparams[["sampleColorList"]][Yparams[["sampleColorList"]] %in% checkVec])
)
names(params[["XYsel"]]) <- unique(Yparams[["XYsel_names"]][Yparams[["XYsel"]] %in% checkVec])
names(params[["allColorOptions"]]) <- Yparams[["allColorOptions_names"]][Yparams[["allColorOptions"]] %in% checkVec]
names(params[["splitOptions"]]) <- Yparams[["splitOptions_names"]][Yparams[["splitOptions"]] %in% checkVec]
names(params[["sampleColorList"]]) <- Yparams[["sampleColorList_names"]][Yparams[["sampleColorList"]] %in% checkVec]
} else {
params <- list(
"XYsel" = c(
names(dfCoordSel)[grep("UMAP", names(dfCoordSel))],
names(dfCoordSel)[grep("tSNE", names(dfCoordSel))],
names(dfCoordSel)[grep("seurat_clusters", names(dfCoordSel))],
names(dfCoordSel)[grep("sub_clusters", names(dfCoordSel))],
names(dfCoordSel)[grep("PC", names(dfCoordSel))],
names(dfCoordSel)[grep("DM_Pseudotime", names(dfCoordSel))],
names(dfCoordSel)[grep("DF_Classification", names(dfCoordSel))],
names(dfCoordSel)[grep("nCount", names(dfCoordSel))],
names(dfCoordSel)[grep("nFeatures", names(dfCoordSel))],
names(dfCoordSel)[grep("percent", names(dfCoordSel))],
names(dfCoordSel)[grep("Con_Prad_AZ", names(dfCoordSel))],
names(dfCoordSel)[grep("Norm_Hyp", names(dfCoordSel))],
names(dfCoordSel)[grep("Gender", names(dfCoordSel))],
names(dfCoordSel)[grep("CellFromTumor", names(dfCoordSel))],
names(dfCoordSel)[grep("Patient", names(dfCoordSel))],
names(dfCoordSel)[grep("Region", names(dfCoordSel))],
names(dfCoordSel)[grep("Article_Cell_Type", names(dfCoordSel))]
),
"allColorOptions" = c(
#"Log10 Expresson" = "lg10Expr",
"DM Pseudotime" = names(dfCoordSel)[grep("DM_Pseudotime", names(dfCoordSel))],
"SampleID" = names(dfCoordSel)[grep("sampleID", names(dfCoordSel))],
"Gender" = names(dfCoordSel)[grep("Gender", names(dfCoordSel))],
"Patient" = names(dfCoordSel)[grep("Patient", names(dfCoordSel))],
"Doublet Classification" = names(dfCoordSel)[grep("DF_Classification", names(dfCoordSel))] ,
"Cluster" = names(dfCoordSel)[grep("seurat_clusters", names(dfCoordSel))] ,
"nCount_RNA" = names(dfCoordSel)[grep("nCount_RNA", names(dfCoordSel))],
"nFeature_RNA" = names(dfCoordSel)[grep("nFeature_RNA", names(dfCoordSel))],
"percent_mt" = names(dfCoordSel)[grep("percent_mt", names(dfCoordSel))],
"S Phase Score" = names(dfCoordSel)[grep("S_Score", names(dfCoordSel))],
"G2M Score" = names(dfCoordSel)[grep("G2M_Score", names(dfCoordSel))],
"Cell Cycle Phase" = names(dfCoordSel)[grep("Phase", names(dfCoordSel))],
"Uniform" = names(dfCoordSel)[grep("all", names(dfCoordSel))]
),
"splitOptions" = c(
#"Log10 Expresson" = "lg10Expr",
"DM Pseudotime" = names(dfCoordSel)[grep("DM_Pseudotime", names(dfCoordSel))],
"SampleID" = names(dfCoordSel)[grep("sampleID", names(dfCoordSel))],
"Gender" = names(dfCoordSel)[grep("Gender", names(dfCoordSel))],
"Patient" = names(dfCoordSel)[grep("Patient", names(dfCoordSel))],
"Doublet Classification" = names(dfCoordSel)[grep("DF_Classification", names(dfCoordSel))] ,
"Cluster" = names(dfCoordSel)[grep("seurat_clusters", names(dfCoordSel))] ,
"nCount_RNA" = names(dfCoordSel)[grep("nCount_RNA", names(dfCoordSel))],
"nFeature_RNA" = names(dfCoordSel)[grep("nFeature_RNA", names(dfCoordSel))],
"percent_mt" = names(dfCoordSel)[grep("percent_mt", names(dfCoordSel))],
"S Phase Score" = names(dfCoordSel)[grep("S_Score", names(dfCoordSel))],
"G2M Score" = names(dfCoordSel)[grep("G2M_Score", names(dfCoordSel))],
"Cell Cycle Phase" = names(dfCoordSel)[grep("Phase", names(dfCoordSel))],
"Uniform" = names(dfCoordSel)[grep("all", names(dfCoordSel))]
)
)
}
print(params)
## ##
###############################################################################
Xchoices <- c("Log10 Expression" = "lg10Expr",
params[["allColorOptions"]],
params[["XYsel"]]
)
if (length(grep("^UMAP_1$", Xchoices)) == 1){
Xsel <- as.vector(Xchoices[grep("^UMAP_1$", Xchoices)])
} else {
Xsel <- as.vector(Xchoices[1])
}
Ychoices <- c("Log10 Expression" = "lg10Expr",
params[["XYsel"]]
)
if (length(grep("^UMAP_2$", Ychoices)) == 1){
Ysel <- as.vector(Ychoices[grep("^UMAP_2$", Ychoices)])
} else {
Ysel <- as.vector(Ychoices[2])
}
splitChoices <- params[["splitOptions"]]
if (length(grep("sampleID", splitChoices)) == 1){
splitSel <- as.vector(splitChoices[grep("sampleID", splitChoices)])
} else {
splitSel <- as.vector(splitChoices[1])
}
colorChoices <- c("Log10 Expression" = "lg10Expr",
params[["allColorOptions"]]
)
if (length(grep("^lg10Expr$", colorChoices)) == 1){
colSel <- as.vector(colorChoices[grep("^lg10Expr$", colorChoices)])
} else {
colSel <- as.vector(colorChoices[1])
}
spectralCols <- c(
Darkred = "#D53E4F",
Red = "#F46D43",
Orange = "#FDAE61" ,
Lightorange = "#FEE08B",
Yellow = "#FFFFBF",
Lightgreen = "#E6F598",
Green = "#ABDDA4",
Darkgreen = "#66C2A5",
Blue = "#3288BD"
)
conditionVec <- unique(sort(dfCoordSel$sampleID))
Nsamples <- length(conditionVec)
## ##
###############################################################################
###############################################################################
## ##
oldw <- getOption("wafrn")
options(warn = -1)
if (mode == "SQLite"){
setwd("data")
dbDB <- dbConnect(RSQLite::SQLite(), dbname=dbname)
setwd("..")
} else {
dbDB <- dbConnect(MySQL(), user = user, password = DBpd, host = host, dbname=dbname)
}
query <- paste0("SELECT DISTINCT gene FROM ", geneID_TbName)
allGenes <- as.vector(dbGetQuery(dbDB, query)[,"gene"])
dbDisconnect(dbDB)
## ##
###############################################################################
###############################################################################
## ##
shinyUI(fluidPage(
navbarPage(
"bioLOGIC SC",
tabPanel("FeatureView"),
tags$head(
tags$style(type = 'text/css',
HTML('.navbar { background-color: #42972050;}
.navbar-default .navbar-brand{color: white;}
.tab-panel{ background-color: red; color: white}
.navbar-default .navbar-nav > .active > a,
.navbar-default .navbar-nav > .active > a:focus,
.navbar-default .navbar-nav > .active > a:hover {
color: #555;
background-color: #42972050;
}')
),
tags$script(HTML("var header = $('.navbar > .container-fluid');
header.append('<div style=\"float:left\"><ahref=\"URL\"><img src=\"assets/images/logo.ico\" alt=\"alt\" style=\"float:right;width:33px;height:41px;padding-top:10px;\"> </a>`</div>');
console.log(header)")
),
tags$link(rel="shortcut icon", href="assets/images/logo.ico")
)
),
#titlePanel("FeatureView"),
sidebarLayout(
sidebarPanel(
tags$style(".well {background-color:#42972050;}"),
helpText("To create a Violin-stype Plot, select for example seurat_clusters as x-axis, lg10Expr as y-Axis and seurat_clusters as colorBy option."),
selectizeInput("gene",
label = "Gene or Category Selection",
choices = NULL, #c(as.vector(sort(unique(allGenes)))),
selected = geneDefault,
options = list(maxOptions = 50)) ,
selectInput("x_axis",
label = "Choose an X-axis",
choices = Xchoices,
selected = Xsel),
selectInput("y_axis",
label = "Choose an Y-axis",
choices =Ychoices,
selected = Ysel),
selectInput("splitByColumn",
label = "Split Plots By",
choices = splitChoices,
selected = splitSel),
selectInput("colorBy",
label = "Color Plots By",
choices = colorChoices,
selected = colSel),
selectInput("dotcolor",
label = "Choose dot colorscale",
choices =c("Darkblue" = "darkblue", spectralCols),
selected = "darkblue"),
selectInput("lowColor",
label = "Choose low colorscale",
choices =c("Grey" = "#D3D3D3", "White" = "white", spectralCols),
selected = "#D3D3D3"),
selectInput("background",
label = "Select Background",
choices =c("Grey" = "grey", "White" = "white","Minimal" = "minimal", "Plain" = "plain"),
selected = "white"),
radioButtons("dotsize", label = "Choose a Dotsize", choices = c("0.1","0.5","1","2"), selected = "1",
inline = FALSE, width = NULL, choiceNames = c("0.1","0.5","1","2"),
choiceValues = c("0.1","0.5","1","2")),
# selectInput("dotsize",
# label = "Choose an Dotsize",
# choices =c("0.1","0.5","1","2"),
# selected = "1"),
#downloadButton('downloadPlot', "Download Plot"),
#downloadButton("downloadData", "Download Data"),
# checkboxGroupInput("selected_sample",
# label = "Select Column",
# choices = seq_along(mtcars))
),
mainPanel(
fluidRow(
column(12,
uiOutput("multi_plot_ui")
)
),
fluidRow(
column(12,
textOutput("dev_text")
)
)
)
)
))
## ##
###############################################################################
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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