Commit ca251050 authored by Etienne Rifa's avatar Etienne Rifa
Browse files

v1.0.1

add information about input table dimension, features/samples omitted for acp
change project name
update readme
parent ebc56532
Package: graphstats
Title: graphstats
Package: graphstatsr
Title: graphstatsr
Version: 1.0.1
Authors@R:
person(given = "Etienne",
......
......@@ -248,6 +248,7 @@ mod_Inputs_server <- function(id, r = r, session = session){
output$prevds1 <- renderPrint({
cat(file = stderr(), 'rendering ds1', "\n")
cat('Running graphstats v1.0.1\n')
cat(glue::glue("Features table with {nrow(dataset1())} rows and {ncol(dataset1())} columns.\n\n"))
head(dataset1()[, 1:6])
if (is.null(dataset1())) {
print("no data")
......@@ -256,10 +257,14 @@ mod_Inputs_server <- function(id, r = r, session = session){
} else{
head(dataset1()[, 1:ncol(dataset1())])
}
})
output$prevmt1 <- renderPrint({
cat(file = stderr(), 'rendering mt1', "\n")
cat(glue::glue("\nMetadata table with {nrow(metadata1())} rows and {ncol(metadata1())} columns.\n\n"))
if (is.null(metadata1())) {
print("no data")
} else if (ncol(metadata1()) > 6) {
......@@ -267,7 +272,8 @@ mod_Inputs_server <- function(id, r = r, session = session){
} else{
head(metadata1()[, 1:ncol(metadata1())])
}
})
# Datatable with reactive filters & button
......@@ -491,6 +497,7 @@ mod_Inputs_server <- function(id, r = r, session = session){
acp_input <- na.omit(r_values$features_final)
r_values$snaomit <- setdiff(row.names(r_values$features_final),row.names(acp_input))
r_values$snaomit_att <- "sample(s)"
r_values$snaomit_ndim <- nrow(r_values$features_final)
}
if(input$naomit_method == 1){
......@@ -499,6 +506,7 @@ mod_Inputs_server <- function(id, r = r, session = session){
acp_input <- t(Tfeat_ok)
r_values$snaomit <- setdiff(row.names(Tfeat),row.names(Tfeat_ok))
r_values$snaomit_att <- "feature(s)"
r_values$snaomit_ndim <- ncol(r_values$features_final)
}
if(nrow(acp_input) == 0){
......@@ -543,7 +551,7 @@ mod_Inputs_server <- function(id, r = r, session = session){
req(r_values$snaomit,r_values$snaomit_att)
cat(file = stderr(), 'missing values', "\n")
list1 <- glue_collapse(r_values$snaomit, ", ")
glue::glue("Following {r_values$snaomit_att} were omitted for PCA:\n{list1}")
glue::glue("Following {r_values$snaomit_att} were omitted for PCA ({length(r_values$snaomit)}/{r_values$snaomit_ndim}):\n{list1}")
})
# Generate ACP Table
......
<!-- README.md is generated from README.Rmd. Please edit that file -->
# graphstats
# GraphstatsR
<!-- badges: start -->
<!-- [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -->
<!-- badges: end -->
A shiny app allowing users to generate advanced interactive graphics and statistical tests.
## Prerequisites
R3.6.3 or upper is required (https://pbil.univ-lyon1.fr/CRAN/bin/)
* Linux
```bash
sudo apt-get install r-base
sudo apt-get install git
```
* Windows
[Rtools](https://cran.r-project.org/bin/windows/Rtools/) and [git](https://git-scm.com/download/win) are required.
## Installation
* In R console:
You can install the released version of graphstats from [this
repository](https://forgemia.inra.fr/etienne.rifa/graphstats) with:
``` r
install.packages("remotes")
remotes::install_gitlab(repo = "etienne.rifa/graphstats", auth_token = 'LgkWC8oPN7aq8bXZ8Cto', host = "forgemia.inra.fr")
remotes::install_gitlab(repo = "etienne.rifa/graphstats", host = "forgemia.inra.fr")
```
## To run Shiny app
## To run Shiny app in R
``` r
# To update app
remotes::install_gitlab(repo = "etienne.rifa/graphstats", host = "forgemia.inra.fr")
# To run app
library(graphstats)
graphstats::run_app()
```
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