Commit 03d848c6 authored by GAREL Marc's avatar GAREL Marc
Browse files

Add Credit part and mod ification of Introduction text in Upload part

parent 851e0209
##################################################
## Project: Shiny app allowing plot and parameters for microbial growth dataset
## Script purpose: Perform logistic regression to estimate growth rate and maximum cells density
## Date: October 2017
## Author: Marc Garel, Severine Martini, Christian Tamburini
##################################################
### libraries
library(shiny)
library(DT)
library(rgl)
library(quantreg)
library(SparseM)
library(rmarkdown)
### ui script
shinyUI(
fluidPage(
navbarPage("Application of a logistic model on microbial datasets",
tabPanel("Upload data",
sidebarLayout(
sidebarPanel("",
fileInput('file1', 'Upload your dataset (.csv or .txt)',
accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv', '.txt')),
# header or not header
checkboxInput('header', 'Header', TRUE),
#
radioButtons('sep', 'Dataset separator',
c(Comma=',', Semicolon=';', Tab='\t'), selected="\t"),
#
radioButtons('dec', 'Decimal separator',
c(Point='.', Comma=','), selected="."),
#
textInput("xlabel", "xlabel", value = "Time (h)"),
#
textInput("ylabel", "ylabel", value = "Biomass")
),
mainPanel(
helpText('This is to perform logistic regression to estimate growth rate and maximum cells density. In order to run this application, you have to format your dataset
with tabulation separators. Also, remove all spaces in the dataset header (prefer to use "_" when needed).
Organise your dataset so that there is only two arrays. The first one being the time and the second the cells density
(e. g. optic density, cell number, biomass). This application proposes a method to perform logistic regression to estimate growth rate as well as maximum cells density.'),
withMathJax(helpText('The logistic equation is define as $$x(t) = r.x_0.(1-\\frac{x_0}K)$$'))
)
)
),
tabPanel("Uploaded data", DT::dataTableOutput("raw_data")),
tabPanel("Plot", plotOutput("raw_plot"), DT::dataTableOutput("parameters"),
downloadButton("downloadData", "Download")),
navbarMenu("Verify parameters estimation",
tabPanel("2D", plotOutput("verify_plot_2D")),
tabPanel("3D", rglwidgetOutput("verify_plot_3D", width = 800, height = 800))),
tabPanel("Citation", verbatimTextOutput("citation"))
)
)
)
##################################################
## Project: Shiny app allowing plot and parameters for microbial growth dataset
## Script purpose: Perform logistic regression to estimate growth rate and maximum cells density
## Date: October 2017
## Author: Marc Garel, Severine Martini, Christian Tamburini
##################################################
### libraries
library(shiny)
library(DT)
library(rgl)
library(quantreg)
library(SparseM)
library(rmarkdown)
### ui script
shinyUI(
fluidPage(
navbarPage("Application of a logistic model on microbial datasets",
tabPanel("Upload data",
sidebarLayout(
sidebarPanel("",
fileInput('file1', 'Upload your dataset (.csv or .txt)',
accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv', '.txt')),
# header or not header
checkboxInput('header', 'Header', TRUE),
#
radioButtons('sep', 'Dataset separator',
c(Comma=',', Semicolon=';', Tab='\t'), selected="\t"),
#
radioButtons('dec', 'Decimal separator',
c(Point='.', Comma=','), selected="."),
#
textInput("xlabel", "xlabel", value = "Time (h)"),
#
textInput("ylabel", "ylabel", value = "Biomass")
),
mainPanel(
helpText('This app is to perform estimation growth rate and maximum cells density using non lineare regression.
The method is detailled in Martini et al. (2013).
In order to run this application, you have to format your dataset with tabulation separators. Also, remove all spaces in the dataset header (prefer to use "_" when needed).
Organise your dataset so that there is only two arrays. The first one being the time and the second the cells density
(e. g. optic density, cell number, biomass). This application proposes a method to perform logistic regression to estimate growth rate as well as maximum cells density.'),
withMathJax(helpText('The logistic equation is define as $$x(t) = r.x_0.(1-\\frac{x_0}K)$$'))
)
)
),
tabPanel("Uploaded data", DT::dataTableOutput("raw_data")),
tabPanel("Plot", plotOutput("raw_plot"), DT::dataTableOutput("parameters"),
downloadButton("downloadData", "Download")),
navbarMenu("Verify parameters estimation",
tabPanel("2D", plotOutput("verify_plot_2D")),
tabPanel("3D", rglwidgetOutput("verify_plot_3D", width = 800, height = 800))),
tabPanel("Citation", verbatimTextOutput("citation")),
tabPanel("Credits", helpText('This App is teamwork between resarcher and student.
The PIs is Marc Garel (MIO-CNRS) and Severine Martini (LOV-CNRS), Marte Vienne (BSc student) improved model with statiscal tools and Lloyd Izard (MSc Student) have developped the app wiht PI'))
)
)
)
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment