Commit 422f4fa1 authored by Brandi Cantarel's avatar Brandi Cantarel

update shiny code, process scripts

parent 5a4a99e9
Pipeline #2905 failed with stage
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......@@ -188,19 +188,26 @@ workflow_parameters:
# The workflow must publish all final output into $baseDir
# Name of the R module that the vizapp will run against
vizapp_r_module: 'R/3.2.1-intel'
vizapp_r_module: 'R/3.4.1-gccmkl'
# List of any CRAN packages, not provided by the modules, that must be made
# available to the vizapp
vizapp_cran_packages:
- sqldf
- crosstalk
- htmltools
- htmlwidgets
- httpuv
- shiny
- Vennerable
- DT
- grid
- gridExtra
- ggplot2
- gplots
- gtools
- RColorBrewer
- tidyverse
# # List of any Bioconductor packages, not provided by the modules, that must be made
......
options("repos"="http://cran.rstudio.com/")
update.packages()
install.packages("sqldf",dep=TRUE)
#install.packages("sqldf",dep=TRUE)
install.packages("gmp",dep=TRUE)
install.packages("shinythemes",dep=TRUE)
install.packages(c('gplots','lattice','latticeExtra','vegan','labdsv','cluster','ggplot2'))
install.packages(c('gplots','lattice','latticeExtra','vegan','labdsv','cluster','ggplot2',"tidyverse"))
install.packages("Vennerable", repos="http://R-Forge.R-project.org",type='source')
source("http://bioconductor.org/biocLite.R")
biocLite(c('graph', 'RBGL', 'RColorBrewer', 'reshape', 'gtools',"edgeR", "DESeq2","qusage","ballgown"))
......@@ -4,9 +4,11 @@ library(qusage)
library(DT)
library(ggplot2)
library(ballgown)
library(sqldf)
library(tidyverse)
library(reshape2)
library("gplots")
library(gridExtra)
library(grid)
shinyServer(function(input, output, session) {
......
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......@@ -12,21 +12,11 @@ output$ui_gc <- renderUI({
tabsetPanel(
tabPanel(
"Gene Compare",
dataTableOutput('gc.stats'),
br(),
plotOutput("plot.gene"),
uiOutput('dlboxplot'),
br(),
textOutput("bxplot.desc"),
br(),
plotOutput("violin.gene"),
uiOutput('dlviolinplot'),
br(),
textOutput("violin.desc")
uiOutput('dlboxplot')
)
)),
tags$style(type='text/css', "#dlboxplot { width:100%;margin-left: 35px;}"),
tags$style(type='text/css', "#dlviolinplot { width:100%;margin-left: 35px;}")
tags$style(type='text/css', "#dlboxplot { width:100%;margin-left: 35px;}")
)
))
......
Subproject commit 0f5e4dca5c3985a7f7b0d409edb5140715b925b8
Subproject commit 7adcb10cc4b0159f22faf630fba29ad31c48bf9d
......@@ -78,7 +78,7 @@ foreach $gene (keys %cts) {
}
$cpm = ($cts{$gene}{$sample}/$total{$sample})*1e6;
push @cpm, sprintf("%.2f",log2($cpm));
push @line, $cts{$gene}{$sample};
push @line, sprintf("%0.f",$cts{$gene}{$sample});
}
my @sortct = sort {$b cmp $a} @cpm;
#next unless ($sortct[0] >= 1);
......
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