Commit 1b47a0b9 authored by fsoubes's avatar fsoubes

modify code

parent 8e0f785c
<div class="btn-group" data-toggle="buttons-radio">
<button id="ds_yes" type="button" class="btn btn-mini active">Yes</button>
<button id="ds_yes" type="button" class="btn btn-mini active">Yes</button>
<button id="ds_no" type="button" class="btn btn-mini">No</button>
</div><br/>
<div class="btn-group" data-toggle="buttons-radio">
<button id="dsw_yes" type="button" class="btn btn-mini active">Yes</button>
<button id="dsw_no" type="button" class="btn btn-mini">No</button>
</div><br/>
<div class="btn-group" data-toggle="buttons-radio">
<button id="fs_8" type="button" class="btn btn-mini">8px</button>
<button id="fs_9" type="button" class="btn btn-mini">9px</button>
<button id="fs_10" type="button" class="btn btn-mini">10px</button>
<button id="fs_11" type="button" class="btn btn-mini">11px</button>
<button id="fs_12" type="button" class="btn btn-mini active">12px</button>
<button id="fs_13" type="button" class="btn btn-mini">13px</button>
<button id="fs_14" type="button" class="btn btn-mini">14px</button>
</div><br/>
</div><br/>
<div class="btn-group" data-toggle="buttons-radio">
<button id="dm_classic" type="button" class="btn btn-mini active">Classic</button>
<button id="dm_edwards" type="button" class="btn btn-mini">Edwards'</button>
</div>
\ No newline at end of file
<div class="btn-group" data-toggle="buttons-radio" >
<button id="dm_classic" class="btn btn-mini active" >Classic</button>
<button id="dm_edwards" class="btn btn-mini">Edwards'</button>
</div>
<!--div class="btn-group" role="group" aria-label="Basic example">
<button type="button" class="btn btn-secondary">Left</button>
<button type="button" class="btn btn-secondary">Middle</button>
<button type="button" class="btn btn-secondary">Right</button>
</div-->
<!--div class="btn-group">
<button class="btn" id="test0" autofocus="true">Mon</button>
<button class="btn" id="test1">Tue</button>
<button class="btn" id="test2">Wed</button>
<button class="btn" id="test3">Thu</button>
<button class="btn" id="test4">Fri</button>
<button class="btn" id="test5">Sat</button>
<button class="btn" id="test6">Sun</button>
</div-->
<div class="btn-group btn-group-toggle" data-toggle="buttons">
<label class="btn btn-secondary active">
<input type="radio" name="options" id="option1" autocomplete="off" checked> Classic
</label>
<label class="btn btn-secondary">
<input type="radio" name="options" id="option2" autocomplete="off"> Edwards
</label>
<label class="btn btn-secondary">
<input type="radio" name="options" id="option3" autocomplete="off"> Radio
</label>
</div>
<div style='margin-top: -10.8%;position:absolute; right:23%;'>
<a class='my-tool-tip' data-toggle="tooltip" data-placement="left" title="Tooltip here"> <!-- The class CANNOT be tooltip... -->
<i class='glyphicon glyphicon-info-sign'></i>
</a>
</div>
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......@@ -21,7 +21,7 @@ inactivity <- "function idleTimer() {
idleTimer();"
#The following html are sourced from https://github.com/aghozlane/shaman/blob/master/css/owncss.R
spincss <- "
#plot-container {
z-index: 0;
......@@ -41,8 +41,8 @@ background-color: #fff;
}
"
Errorcss <-
".shiny-output-error { visibility: visible; color: #3c8dbc;}
Errorcss <-
".shiny-output-error { visibility: visible; color: orange; font-size: larger;}
.shiny-output-error:before {
color: #3c8dbc;
......@@ -90,40 +90,24 @@ margin-bottom: -40px;
#' addNews is a function that render a pretty table for news
#'
#' @param date
#' @param title
#' @param text
#' @author Amine Ghozlane
#' @param date
#' @param title
#' @param text
#' @author Amine Ghozlane
#' Source https://github.com/aghozlane/shaman/blob/master/Rfunctions/Data_Management.R
#'
#' @return
#' @export
#'
#' @examples
#'
#'
addNews <- function(date ="",title="",text="")
{
res=list()
res$r1 = paste("<b><font size='+1'>",date,"</font></b>", " - ", "<b><font size='+1'>",title,"</font></b><br/>")
res$r2 = paste("<p><font color='grey'>",text,"</font></p><hr/>")
return(HTML(unlist(res)))
}
#InfoBoxCSS <- "
#.info-box:hover,
#.info-box:hover .info-box-icon {
#background-color: #aaa !important;
#}
#.info-box:active,
#.info-box:active .info-box-icon {
#background-color: #ccc !important;
#}
#"
......@@ -18,7 +18,7 @@ ul li {
position: static;
font-size: 18px;
}
}
.skin-blue .sidebar-menu > li.active > a,.skin-blue .sidebar-menu > li:hover > a {
color:#fff;
......@@ -41,6 +41,10 @@ h2 {
font-size: 20px;
}
#warningsheat {
background-color: #ecf0f5;
border: 1px solid #ecf0f5;
}
p {
/*
......@@ -54,7 +58,6 @@ p {
}
.skin-blue .main-header .logo {
background-color:#1D4D68;
}
......@@ -79,20 +82,38 @@ p {
height: 30%;
}
#advancedjvenn .btn{
border: none;
outline: none;
padding: 6px 11px;
cursor: pointer;
background-color: #337ab7;
}
#advancedjvenn .btn:hover .btn:active {
background-color: #666;
color: white;
}
#advancedjvenn .activate, .btn:hover , .activated {
background-color: #666;
color: white;
}
#advancedjvenn .btn:focus {
outline: none;
}
#advancedjvenn .élément{
color:black;
}
#advancedjvenn .active, .btn:hover {
#advancedjvenn .active .btn-mini:hover .btn-mini:focus {
background-color: #666;
color: white;
}
......@@ -232,4 +253,7 @@ div.outer {
bottom: 0px;
}
a.my-tool-tip, a.my-tool-tip:hover, a.my-tool-tip:visited {
color: black;
}
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......@@ -188,7 +188,7 @@ davidquery <- function(entrezids, species, mycat) {
setCurrentSpecies(object = david, species = specieLocation)
#setCurrentBackgroundPosition(object = david, position = backgroundLocation)
#getSpecieNames(david)
setAnnotationCategories(david, mycat) #c("GOTERM_MF_ALL", "GOTERM_CC_ALL", "GOTERM_BP_ALL")) # "KEGG_PATHWAY"
setAnnotationCategories(david, mycat) #c("GOTERM_MF_ALL", "GOTERM_CC_ALL", "GOTERM_BP_ALL")) "KEGG_PATHWAY"
mydav = as.data.frame(cbind(getFunctionalAnnotationChart(object=david, threshold=1, count=0L))) %>%
filter(Count>1) %>% arrange(desc(Count)) %>% dplyr::select( Category:Count, List.Total:Pop.Total,X.,PValue,Genes,Fold.Enrichment, Bonferroni, Benjamini)
colnames(mydav)[[7]] = "percent"
......@@ -219,11 +219,10 @@ davidqueryvenn <- function(entrezids, species){
)
selectedSpecie = (species)
#setAnnotationCategories(david, c("GOTERM_BP_ALL"))
#backgroundLocation = grep(selectedSpecie,RDAVIDWebService::getBackgroundListNames(david))
specieLocation = grep(selectedSpecie, RDAVIDWebService::getSpecieNames(david))
setCurrentSpecies(object = david, species = specieLocation)
# get the cluster report for the upload
getClusterReport(david, type = "Term")
}
......
......@@ -94,7 +94,7 @@ Vennlist <- function(adj,fc, regulation, cutoffpval, cutofffc){ ## ajout de fore
if(is.null(adj))
return(NULL)
reguser = ifelse(regulation == "up", T, F)
reguserboth = ifelse(regulation == "both", T, F)
lapply(1:ncol(adj), FUN = function(x){
......@@ -347,7 +347,7 @@ toJvenn <- function(myven, adj){
#'
#'
topngenes <- function(dfinter, mycont, inputtop, meandup = "probes", mean = F) {
topngenes <- function(dfinter, mycont, inputtop, meandup = "probes", mean = F ) {
if(meandup == "probes")
......@@ -379,16 +379,15 @@ topngenes <- function(dfinter, mycont, inputtop, meandup = "probes", mean = F) {
return(x)})
reshp <-melt(dfinter[1:inputtop, ],
id.vars = "GeneName",measure.vars = c (mycont),
variable.name = "Comparisons",value.name = "logFC"
)
variable.name = "Comparisons",value.name = "logFC") %>% na.omit()
reshp <- droplevels(reshp)
reshp$GeneName <-factor(reshp$GeneName, levels = unique(as.character(reshp$GeneName)))
p <- ggplot(reshp, aes(
x = GeneName,
y = as.numeric(as.character(formatC(as.double(logFC), digits = 1, format = "f"))),
......
......@@ -10,7 +10,7 @@
options(shiny.maxRequestSize=128000000)
options(digits=3)
cutheatmlist = list( Boxplot = c( `True` = 'Boxplot'), Heatmap=c(`True` = "Heatmap"),
cutheatmlist = list( Boxplot = c( `True` = 'Boxplot'), Heatmap=c(`True` = "Heatmap"),
Stripchart=c(`Without boxplot`="LB", `With boxplot` = "WB"))
......@@ -20,19 +20,16 @@ categoerygen = c( `BP`= "GOTERM_BP_ALL", `MF` = "GOTERM_MF_ALL", `CC`= "GOTERM_
#sudo apt-get install libv8-dev
list.of.packages <- c("AnnotationDbi","shiny","shinythemes","shinyjs","ggplot2","shinyBS","plyr","shinyFiles",
"BH","data.table","DT","readr","colourpicker","shinydashboard","shinytoastr",
"BH","data.table","DT","readr","colourpicker","shinydashboard","heatmaply",
"tools","devEMF","R.devices","FactoMineR","factoextra","gplots","V8",
"RColorBrewer","foreach","doParallel","VennDiagram","gridExtra","plotly","dplyr","reticulate","Hmisc")
"RColorBrewer","foreach","doParallel","gridExtra","plotly","dplyr","reticulate","Hmisc")
#"goseq","GO.db","rbenchmark","heatmaply"
#AnnotationDbi
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)
lapply(list.of.packages,function(x){
suppressPackageStartupMessages(library(x,character.only=TRUE))})
suppressPackageStartupMessages(library(x,character.only=TRUE))})
library(shinyFiles)
source("function/delayinput.R")
......@@ -101,6 +98,6 @@ palette = brewer.pal(8,"Dark2") %>%
textInputRow<-function (inputId, label, value = "") {
div(style="display:inline-block",
tags$label(label, `for` = inputId),
tags$label(label, `for` = inputId),
tags$input(id = inputId, type = "text", value = value,class="input-small"))
}
CREDITS
Pipeline HTML CSS Template
http://www.templatemo.com/tm-496-pipeline
Bootstrap
http://getbootstrap.com/
Images
http://unsplash.com/
Bubba Image Hover Effect
http://tympanus.net/Development/HoverEffectIdeas/
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/* Magnific Popup CSS */
.mfp-bg {
top: 0;
left: 0;
width: 100%;
height: 100%;
z-index: 1042;
overflow: hidden;
position: fixed;
background: #0b0b0b;
opacity: 0.8;
filter: alpha(opacity=80); }
.mfp-wrap {
top: 0;
left: 0;
width: 100%;
height: 100%;
z-index: 1043;
position: fixed;
outline: none !important;
-webkit-backface-visibility: hidden; }
.mfp-container {
text-align: center;
position: absolute;
width: 100%;
height: 100%;
left: 0;
top: 0;
padding: 0 8px;
-webkit-box-sizing: border-box;
-moz-box-sizing: border-box;
box-sizing: border-box; }
.mfp-container:before {
content: '';
display: inline-block;
height: 100%;
vertical-align: middle; }
.mfp-align-top .mfp-container:before {
display: none; }
.mfp-content {
position: relative;
display: inline-block;
vertical-align: middle;
margin: 0 auto;
text-align: left;
z-index: 1045; }
.mfp-inline-holder .mfp-content,
.mfp-ajax-holder .mfp-content {
width: 100%;
cursor: auto; }
.mfp-ajax-cur {
cursor: progress; }
.mfp-zoom-out-cur, .mfp-zoom-out-cur .mfp-image-holder .mfp-close {
cursor: -moz-zoom-out;
cursor: -webkit-zoom-out;
cursor: zoom-out; }
.mfp-zoom {
cursor: pointer;
cursor: -webkit-zoom-in;
cursor: -moz-zoom-in;
cursor: zoom-in; }
.mfp-auto-cursor .mfp-content {
cursor: auto; }
.mfp-close,
.mfp-arrow,
.mfp-preloader,
.mfp-counter {
-webkit-user-select: none;
-moz-user-select: none;
user-select: none; }
.mfp-loading.mfp-figure {
display: none; }
.mfp-hide {
display: none !important; }
.mfp-preloader {
color: #CCC;
position: absolute;
top: 50%;
width: auto;
text-align: center;
margin-top: -0.8em;
left: 8px;
right: 8px;
z-index: 1044; }
.mfp-preloader a {
color: #CCC; }
.mfp-preloader a:hover {
color: #FFF; }
.mfp-s-ready .mfp-preloader {
display: none; }
.mfp-s-error .mfp-content {
display: none; }
button.mfp-close,
button.mfp-arrow {
overflow: visible;
cursor: pointer;
background: transparent;
border: 0;
-webkit-appearance: none;
display: block;
outline: none;
padding: 0;
z-index: 1046;
-webkit-box-shadow: none;
box-shadow: none; }
button::-moz-focus-inner {
padding: 0;
border: 0; }
.mfp-close {
width: 44px;
height: 44px;
line-height: 44px;
position: absolute;
right: 0;
top: 0;
text-decoration: none;
text-align: center;
opacity: 0.65;
filter: alpha(opacity=65);
padding: 0 0 18px 10px;
color: #FFF;
font-style: normal;
font-size: 28px;
font-family: Arial, Baskerville, monospace; }
.mfp-close:hover,
.mfp-close:focus {
opacity: 1;
filter: alpha(opacity=100); }
.mfp-close:active {
top: 1px; }
.mfp-close-btn-in .mfp-close {
color: #333; }
.mfp-image-holder .mfp-close,
.mfp-iframe-holder .mfp-close {
color: #FFF;
right: -6px;
text-align: right;
padding-right: 6px;
width: 100%; }
.mfp-counter {
position: absolute;
top: 0;
right: 0;
color: #CCC;
font-size: 12px;
line-height: 18px;
white-space: nowrap; }
.mfp-arrow {
position: absolute;
opacity: 0.65;
filter: alpha(opacity=65);
margin: 0;
top: 50%;
margin-top: -55px;
padding: 0;
width: 90px;
height: 110px;
-webkit-tap-highlight-color: transparent; }
.mfp-arrow:active {
margin-top: -54px; }
.mfp-arrow:hover,
.mfp-arrow:focus {
opacity: 1;
filter: alpha(opacity=100); }
.mfp-arrow:before,
.mfp-arrow:after,
.mfp-arrow .mfp-b,
.mfp-arrow .mfp-a {
content: '';
display: block;
width: 0;
height: 0;
position: absolute;
left: 0;
top: 0;
margin-top: 35px;
margin-left: 35px;
border: medium inset transparent; }
.mfp-arrow:after,
.mfp-arrow .mfp-a {
border-top-width: 13px;
border-bottom-width: 13px;
top: 8px; }
.mfp-arrow:before,
.mfp-arrow .mfp-b {
border-top-width: 21px;
border-bottom-width: 21px;
opacity: 0.7; }
.mfp-arrow-left {
left: 0; }
.mfp-arrow-left:after,
.mfp-arrow-left .mfp-a {
border-right: 17px solid #FFF;
margin-left: 31px; }
.mfp-arrow-left:before,
.mfp-arrow-left .mfp-b {
margin-left: 25px;
border-right: 27px solid #3F3F3F; }
.mfp-arrow-right {
right: 0; }
.mfp-arrow-right:after,
.mfp-arrow-right .mfp-a {
border-left: 17px solid #FFF;
margin-left: 39px; }
.mfp-arrow-right:before,
.mfp-arrow-right .mfp-b {
border-left: 27px solid #3F3F3F; }
.mfp-iframe-holder {
padding-top: 40px;
padding-bottom: 40px; }
.mfp-iframe-holder .mfp-content {
line-height: 0;
width: 100%;
max-width: 900px; }
.mfp-iframe-holder .mfp-close {
top: -40px; }
.mfp-iframe-scaler {
width: 100%;
height: 0;
overflow: hidden;
padding-top: 56.25%; }
.mfp-iframe-scaler iframe {
position: absolute;
display: block;
top: 0;
left: 0;
width: 100%;
height: 100%;
box-shadow: 0 0 8px rgba(0, 0, 0, 0.6);
background: #000; }
/* Main image in popup */
img.mfp-img {
width: auto;
max-width: 100%;
height: auto;
display: block;
line-height: 0;
-webkit-box-sizing: border-box;
-moz-box-sizing: border-box;
box-sizing: border-box;
padding: 40px 0 40px;
margin: 0 auto; }
/* The shadow behind the image */
.mfp-figure {
line-height: 0; }
.mfp-figure:after {
content: '';
position: absolute;
left: 0;
top: 40px;
bottom: 40px;
display: block;
right: 0;
width: auto;
height: auto;
z-index: -1;
box-shadow: 0 0 8px rgba(0, 0, 0, 0.6);
background: #444; }
.mfp-figure small {
color: #BDBDBD;
display: block;
font-size: 12px;
line-height: 14px; }
.mfp-figure figure {
margin: 0; }
.mfp-bottom-bar {
margin-top: -36px;
position: absolute;
top: 100%;
left: 0;
width: 100%;
cursor: auto; }
.mfp-title {
text-align: left;
line-height: 18px;
color: #F3F3F3;
word-wrap: break-word;
padding-right: 36px; }
.mfp-image-holder .mfp-content {
max-width: 100%; }
.mfp-gallery .mfp-image-holder .mfp-figure {
cursor: pointer; }
@media screen and (max-width: 800px) and (orientation: landscape), screen and (max-height: 300px) {
/**
* Remove all paddings around the image on small screen
*/
.mfp-img-mobile .mfp-image-holder {
padding-left: 0;
padding-right: 0; }
.mfp-img-mobile img.mfp-img {
padding: 0; }
.mfp-img-mobile .mfp-figure:after {
top: 0;
bottom: 0; }
.mfp-img-mobile .mfp-figure small {
display: inline;
margin-left: 5px; }
.mfp-img-mobile .mfp-bottom-bar {
background: rgba(0, 0, 0, 0.6);
bottom: 0;
margin: 0;
top: auto;
padding: 3px 5px;
position: fixed;
-webkit-box-sizing: border-box;
-moz-box-sizing: border-box;
box-sizing: border-box; }
.mfp-img-mobile .mfp-bottom-bar:empty {
padding: 0; }
.mfp-img-mobile .mfp-counter {