.Rhistory

runApp('F:/master/CilioGenics-website')
shiny::runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
remove.packages("geneName")
library(devtools)
install_github("mustafapir/geneName")
library(geneName)
xx<-geneName::hgnc
View(xx)
View(xx)
con <- dbConnect(RMySQL::MySQL(), group = "user", dbname = 'ciliogenics')
library(RMySQL)
con <- dbConnect(RMySQL::MySQL(), group = "user", dbname = 'ciliogenics')
con <- dbConnect(RMySQL::MySQL(), group = "user", dbname = 'ciliogenics', port = 3306)
con <- dbConnect(RMySQL::MySQL(), group = 'user', dbname = 'ciliogenics')
con <- dbConnect(RMySQL::MySQL(), host = "host", user = "user", password = "password", dbname = 'ciliogenics', port = 3306)
Sys.getenv("password")
shiny::runApp('F:/master/CilioGenics-website')
View(pub_mat)
pub_mat[,-1]==0
all(pub_mat[,-1])==0
all(pub_mat[,-1] == 0)
which(sum(pub_mat)==0)
which(sum(pub_mat[,-1])==0)
sum(pub_mat[15,-1])
apply(pub_mat[,-1],2,sum)
which(apply(pub_mat[,-1],2,sum))
which(apply(pub_mat[,-1],2,sum) == 88)
which(apply(pub_mat[,-1],1,sum) == 0)
pub_mat[which(apply(pub_mat[,-1],1,sum) == 0)]
pub_mat[which(apply(pub_mat[,-1],1,sum) == 0),]
runApp('F:/master/CilioGenics-website')
View(pub_mat)
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
?main_heatmap
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
shiny::runApp('F:/master/CilioGenics-website')
runApp('C:/Users/phago/Desktop/ziya/DENEME2.R')
runApp('C:/Users/phago/Desktop/ziya/DENEME2.R')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('C:/Users/phago/Desktop/ziya/DENEME2.R')
runApp('C:/Users/phago/Desktop/ziya/DENEME2.R')
runApp('F:/master/CilioGenics-website')
runApp('C:/Users/phago/Desktop/ziya/DENEME2.R')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('C:/Users/phago/Desktop/ziya/DENEME2.R')
shiny::runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
div(br(),br(),
tags$style(type = "text/css", "#q1 {vertical-align: top;}"),
tippy(bsButton("tooltipbutton", label = "", icon = icon("question"), style = "info", size = "extra-small"),
sprintf("<span style='font-size:15px;'>%s<span>", tooltip), placement = "top", animation = "scale", arrow = TRUE, theme = "blue"),
br(),
value
)
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp()
runApp('F:/master/CilioGenics-website')
runApp()
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
shiny::runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
install.packages("magick")
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
Heatmap(as.matrix(pub_genes[,-1]),
rect_gp = gpar(col = "white", lwd = 2), row_gap = unit(5, "mm"),
cluster_row_slices = FALSE, cluster_rows = FALSE, cluster_columns = FALSE, col = col_fun,
height = unit(8, "cm"), show_heatmap_legend = FALSE, column_names_side = "bottom",
heatmap_height = unit(100, "npc"), show_row_names = FALSE, use_raster = FALSE)
Heatmap(as.matrix(pub_genes[1:1000,-1]),
rect_gp = gpar(col = "white", lwd = 2), row_gap = unit(5, "mm"),
cluster_row_slices = FALSE, cluster_rows = FALSE, cluster_columns = FALSE, col = col_fun,
height = unit(8, "cm"), show_heatmap_legend = FALSE, column_names_side = "bottom",
heatmap_height = unit(100, "npc"), show_row_names = FALSE, use_raster = FALSE)
Heatmap(as.matrix(pub_genes[1:100,-1]),
rect_gp = gpar(col = "white", lwd = 2), row_gap = unit(5, "mm"),
cluster_row_slices = FALSE, cluster_rows = FALSE, cluster_columns = FALSE, col = col_fun,
height = unit(8, "cm"), show_heatmap_legend = FALSE, column_names_side = "bottom",
heatmap_height = unit(100, "npc"), show_row_names = FALSE, use_raster = FALSE)
Heatmap(as.matrix(pub_genes[1:100,-1]),
rect_gp = gpar(col = "white", lwd = 2), row_gap = unit(5, "mm"),
cluster_row_slices = FALSE, cluster_rows = FALSE, cluster_columns = FALSE, col = col_fun,
height = unit(100, "cm"), show_heatmap_legend = FALSE, column_names_side = "bottom",
heatmap_height = unit(100, "npc"), show_row_names = FALSE, use_raster = FALSE)
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('C:/Users/phago/Desktop/ziya/DENEME2.R')
runApp('C:/Users/phago/Desktop/ziya/DENEME2.R')
runApp('C:/Users/phago/Desktop/ziya/DENEME2.R')
runApp('C:/Users/phago/Desktop/ziya/DENEME2.R')
runApp('C:/Users/phago/Desktop/ziya/DENEME2.R')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-shinyapps')
dropdownBlock()
dropdownBlock
runApp('F:/master/CilioGenics-shinyapps')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
shinyloadtest::record_session("http://127.0.0.1:7743")
shinyloadtest::record_session("http://127.0.0.1:7743")
library(shiny)
library(shinydashboard)
library(shinydashboardPlus)
runApp('F:/master/CilioGenics-website')
runApp()
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
install.packages("shiny.semantic")
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('C:/Users/phago/Desktop/ziya/DENEME2.R')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('F:/master/semantic_ciliogenics')
runApp('C:/Users/phago/Desktop/ziya/DENEME2.R')
runApp('F:/master/CilioGenics-website')
shiny::runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
searchInput2<-function (inputId, label = NULL, value = "", placeholder = NULL,
btnSearch = NULL, btnReset = NULL, resetValue = "", width = NULL)
{
value <- shiny::restoreInput(id = inputId, default = value)
if (!is.null(btnSearch)) {
btnSearch <- htmltools::tags$button(class = "btn btn-default btn-addon action-button",
id = paste0(inputId, "_search"), type = "button",
btnSearch)
}
if (!is.null(btnReset)) {
btnReset <- htmltools::tags$button(class = "btn btn-default btn-addon action-button",
id = paste0(inputId, "_reset"), type = "button",
btnReset)
}
css_btn_addon <- paste0(".btn-addon{", "font-size:14.5px;",
"margin:0 0 0 0 !important;", "display: inline-block !important;",
"}")
searchTag <- htmltools::tags$li(class = "form-group shiny-input-container",
style = if (!is.null(width))
paste0("width: ", validateCssUnit(width), ";"),
if (!is.null(label))
htmltools::tags$label(label, `for` = inputId), htmltools::tags$div(id = inputId,
`data-reset` = !is.null(resetValue), `data-reset-value` = resetValue,
class = "input-group search-text", htmltools::tags$input(id = paste0(inputId,
"_text"), style = "border-radius: 0.25em 0 0 0.25em !important;",
type = "text", class = "form-control", value = value,
placeholder = placeholder), htmltools::tags$div(class = "input-group-btn",
btnReset, btnSearch)), singleton(tags$head(tags$style(css_btn_addon))))
attachShinyWidgetsDep(searchTag)
}
runApp('F:/master/CilioGenics-website')
searchInput2<-function (inputId, label = NULL, value = "", placeholder = NULL,
btnSearch = NULL, btnReset = NULL, resetValue = "", width = NULL)
{
value <- shiny::restoreInput(id = inputId, default = value)
if (!is.null(btnSearch)) {
btnSearch <- htmltools::tags$button(class = "btn btn-default btn-addon action-button",
id = paste0(inputId, "_search"), type = "button",
btnSearch)
}
if (!is.null(btnReset)) {
btnReset <- htmltools::tags$button(class = "btn btn-default btn-addon action-button",
id = paste0(inputId, "_reset"), type = "button",
btnReset)
}
css_btn_addon <- paste0(".btn-addon{", "font-size:14.5px;",
"margin:0 0 0 0 !important;", "display: inline-block !important;",
"}")
searchTag <- htmltools::tags$div(class = "form-group shiny-input-container",
style = if (!is.null(width))
paste0("width: ", validateCssUnit(width), ";"),
if (!is.null(label))
htmltools::tags$label(label, `for` = inputId), htmltools::tags$div(id = inputId,
`data-reset` = !is.null(resetValue), `data-reset-value` = resetValue,
class = "input-group search-text", htmltools::tags$input(id = paste0(inputId,
"_text"), style = "border-radius: 0.25em 0 0 0.25em !important;",
type = "text", class = "form-control", value = value,
placeholder = placeholder), htmltools::tags$div(class = "input-group-btn",
btnReset, btnSearch)), singleton(tags$head(tags$style(css_btn_addon))))
attachShinyWidgetsDep(searchTag)
}
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
shiny::runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
!div()
!div
?div
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
shiny::runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
shiny::runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
shiny::runApp('F:/master/CilioGenics-website')
shiny::runApp('F:/master/CilioGenics-website')
shiny::runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
lung<-readRDS("./data/lung_orig.RDS")
setwd("F:/master/CilioGenics-website")
lung<-readRDS("./data/lung_orig.RDS")
DimPlot(object = pbmc, reduction = "umap")
library(Seurat)
DimPlot(object = pbmc, reduction = "umap")
DimPlot(object = lung, reduction = "umap")
FeaturePlot(object = lung, features = "ARL13B")
FeaturePlot(object = lung, features = "TMEM145")
FeaturePlot(object = lung, features = "ELMOD3")
FeaturePlot(object = lung, features = "FOXJ1")
library(shiny)
library(ggplot2)
rownames(lung)
runApp()
genelist_lung<-rownames(lung)
class(genelist_lung)
length(genelist_lung)
genelist_lung[1]
genelist_lung[2]
c(genelist_lung)
runApp()
runApp()
runApp()
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp('F:/master/CilioGenics-website')
runApp()
Idents(object = lung)
head(Idents(object = lung))
xx<-Idents(object = lung)
class(xx)
levels(xx)
subset(x = lung, idents = "Ciliated")
runApp()
runApp()
aa<-subset(x = lung, idents = "Ciliated")
rownames(aa)
length(rownames(aa))
length(rownames(lung))
markers<-readRDS("markers.RDS")
markers<-readRDS("./data/markers.RDS")
a<-markers[1]
a<-markers[[1]]
a<-markers[[ciliary_markers]]
markers[[which(a == "Ciliated")]]
a<-levels(lung)
markers[[which(a == "Ciliated")]]
runApp()
runApp()
runApp()
a<-levels(lung)
reactable(
markers[[which(a == "Ciliated")]], resizable = TRUE, filterable = TRUE,
searchable = TRUE, defaultPageSize = 10, showPageSizeOptions = TRUE,
highlight = TRUE
)
class(markers[[which(a == "Ciliated")]])
runApp()
runApp()
runApp()
runApp()
a<-levels(lung)
i<-which(a == "Ciliated")
i
class(i)
hey<-markers[[i]]
hey
reactable(
hey, resizable = TRUE, filterable = TRUE,
searchable = TRUE, defaultPageSize = 10, showPageSizeOptions = TRUE,
highlight = TRUE
)
runApp()
runApp()
runApp()
runApp()
runApp()
runApp()
runApp()
runApp()