BLUE_Hs_time.Rmd.bu

---
title: "BLUE Human 3-6hrs. VS 0hrs."
output: 
  flexdashboard::flex_dashboard:
     navbar:
      - { title: "Ca TR VS FP", href: "BLUE_ca_TRVFP.html" , align: "right"}
      - { title: "Ca 6-24hr VS 3hr", href: "BLUE_ca_time.html" , align: "right"}
      - { title: "Ca CEC3609 V CEC3672", href: "BLUE_ca_3609V3672.html" , align: "right"}
      - { title: "Hs CEC3609 V CEC3672", href: "BLUE_Hs_3609V3672.html" , align: "right"}
      - { title: "Main", href: "index.html" , align: "right"}
    # self_contained: F
    # vertical_layout: scroll
# source: embed
# widescreen: true
# fig_width: 7
# fig_height: 6
# fig_caption: true
df_print: kable
# css: https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css
---

```{r setup, include=FALSE}

knitr::opts_chunk$set(echo = FALSE)
options(knitr.duplicate.label = "allow")
# Path and file names
# root folder
RootFolder=dirname(rstudioapi::getSourceEditorContext()$path)
setwd(RootFolder)

# Load home made function and variable and libraries
source(file.path("R", "RTools.R"))
source(file.path("R","20200610-DGE_library_functions.R"))
source(file.path("R","GO.R"))
library(data.table)
library(knitr)
library(kableExtra)
library(ggsignif)
library(ggpubr)
library(grid)
library(gridExtra)
library(RColorBrewer)
library(org.Hs.eg.db)
library(crosstalk)
# Check Ca GO db is install 
Data_dir=file.path("Data")

if( ! require( "org.Calbicans.eg.db" , character.only = TRUE ) ){
  BuildCaGOdb_CP(OuputDir = Data_dir)
  install.packages(file.path(Data_dir,"org.Calbicans.eg.db"),repos = NULL)
}
```

Normalisation {.storyboard}
=====================================

```{r Var Hs BRAUN}
Pair="BLUE"
# Path and file names
# root folder
# RootFolder="/media/edurandau/DATA/Eric_Durandau/Sanglard/Labbook/Workbench/Bioinformatics/GREEN-BRAUN-data_exploration/Tests"
# Output subfolder name
# OutputFolder="Hs_3-6h_V_0h"
# Outputfolder path
# OutputFolderPath=file.path(RootFolder,OutputFolder)

# Raw data table
Path2Data=file.path(Data_dir,"20210611-Hs_BLUE_Raw_ReadCount.tsv")
# Table containing the list of sample ID and coresponding real names
Path2SubTbl=file.path(Data_dir,"BLUE_SampleInfos.tsv")
# Read count table with corrected sample names
RC_correctedSampleNames=paste0(Pair,"Hs_CountTable_SampleNames.tbl",collapse = "_")

LoadDataFn=LoadRawReadCountsHs
# Variable related to Normalisation, Differential expression analysis, clustering and the GO part
# NORMALISATION
# RegEx pattern enabling to extract the MetaData from samples real names
RegexPattern="(?<Isolate>\\w{3}\\d{4})_(?<replicate>\\d{1})_(?<condition>\\w{2})_(?<time>\\d{1,2y})"
# RegEx pattern enabling to remove some sample from the analysis
# ExcludeSampleRegex="(?<Isolate>\\w{3}(3621|3678))_(?<replicate>\\d+)"
ExcludeSampleRegex="(_NI)"
# Metadata column to conserve in the "Genes" table. Renames the column to make it compatible with HomeMade functions
GenesMetaData=c("Gene", "ORF19_ID","ASSEMBLY22_ID","Chr","Start", "End","Length","EntrezID","Note")
Colnames4Genes=GenesMetaData
# Additional factor for the normalisation and DE
AdditionalFact=c("time", "Isolate")
# pattern to extract chromosome name
Pattern_X="\\w+"
```


```{r BRAUN Hm normalisation, child="R/20210526-Normalisation.Rmd"}
```

Differential gene expression analysis {.storyboard}
=====================================

```{r setup DEG Hm Time}

# DEG
NameSharedData="Hm_time"
  # Variable for the contrast map to define the comparaison to perform
DE_Contrast_Cond=AdditionalFact
Ref=c( 0,"CEC3605")
# Sample="Conditions"
  # Select the main comparaison variable
MainComparaison="time"
SecondaryComparaison=AdditionalFact
  # define the log2FC cutoff and the pvalue cutoff
LFC_Cutoff=0.5
pVal_Cutoff=0.05
# Clustering
  # Number of cluster
ClustNumb=4
  # distance method
DistMethod="manhattan"
  # agglomeration method
AggloMethod="centroid"
  # Decide Cutoff. for example if 3 , gene is selected if differentially expressed in 1/3 of comparisons
Factor_Numb_Conditions_gene_diff_expressed=3

```



```{r KnitDEG Hm Time, child="R/20210526-DEG.Rmd"}
```


GO
=====================================


```{r GO Hm TR-FP setup}
#  GO enrichment
# library(org.Calbicans.eg.db)
#  GO enrichment
library(org.Hs.eg.db)
OrgDb=org.Hs.eg.db
keytype="ENTREZID"
GO_pValue=0.1
GO_qValue=GO_pValue
MinGO=10
MaxGO=500
# STRING
STRING_DB=string_db_Hs
StringConnection=50
```

```{r prepare Go hs time, child="R/20210608-GO.Rmd"}
```

```{r Plot GO Hs time, child="R/20210608-GO_Plots_Interactive.Rmd"}
```

Gene Networks
=====================================

Column {.tabset}
-------------------------------------

```{r Plot GO hs time,  comment='', echo=FALSE, message=FALSE, warning=FALSE, results="asis"}
out = NULL
for (i in ClustersID) {
  C=i
  if (length(PlotList[[as.character(C)]])<2){
    print("No GO emerge from that list of gene")
  }else{
    out <- c(out, knit_child(file.path("R",'20210608-GO_Plots.Rmd'), quiet=TRUE))
  }
}
cat(knit(text=unlist(paste(out, collapse = '\n')), quiet=TRUE))

```