diff --git a/inst/rmarkdown/templates/reportbis/resources/template.tex b/inst/rmarkdown/templates/reportbis/resources/template.tex
new file mode 100644
index 0000000000000000000000000000000000000000..bb4e2aa0fa3b3f387ec8cf11225f2b2ad820ef6f
--- /dev/null
+++ b/inst/rmarkdown/templates/reportbis/resources/template.tex
@@ -0,0 +1,6 @@
+% !TeX root = wrapper.tex
+\title{$title$}
+\author{by $for(author)$$author.name$$sep$, $endfor$}
+
+\maketitle
+
diff --git a/inst/rmarkdown/templates/reportbis/resources/wrapper.tex b/inst/rmarkdown/templates/reportbis/resources/wrapper.tex
new file mode 100644
index 0000000000000000000000000000000000000000..cf979f9b26fdf5762974646aa5344afe5a0bd708
--- /dev/null
+++ b/inst/rmarkdown/templates/reportbis/resources/wrapper.tex
@@ -0,0 +1,27 @@
+\documentclass[a4paper]{report}
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{nips_2017}
+\usepackage{amsmath,amssymb,array}
+\usepackage{booktabs}
+
+\providecommand{\tightlist}{%
+ \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+
+%% load any required packages here
+$preamble$
+
+\begin{document}
+
+%% do not edit, for illustration only
+\sectionhead{Contributed research article}
+\volume{XX}
+\volnumber{YY}
+\year{20ZZ}
+\month{AAAA}
+
+\begin{article}
+ \input{$filename$}
+\end{article}
+
+\end{document}
\ No newline at end of file
diff --git a/inst/rmarkdown/templates/reportbis/skeleton/.Rhistory b/inst/rmarkdown/templates/reportbis/skeleton/.Rhistory
new file mode 100644
index 0000000000000000000000000000000000000000..c489c74f3cdee26478271cc4dba144e958d16b3c
--- /dev/null
+++ b/inst/rmarkdown/templates/reportbis/skeleton/.Rhistory
@@ -0,0 +1,512 @@
+# BIGZ[grep("reg09", rsid),1:3] <- NA
+# BIGZ[grep("reg10", rsid),4:6] <- NA
+rownames(BIGZ) <- rsid
+# What does it look like ?
+require(pheatmap)
+png("zscores.png", res = 100)
+pheatmap(BIGZ, cluster_rows = FALSE, cluster_cols = FALSE, cellwidth = 10, cellheight = 10)
+dev.off()
+# Create regions
+# Create Z scores
+# Write covariance matrix
+write.table(data.frame(ID=ids, COV), file="COV.txt", row.names = F, quote=F, sep="\t")
+# Write region file
+regions <- data.frame(chr=sprintf("chr%i", rep(1:5,e=2)),
+start=rep(c(1,4),5),
+stop=rep(c(3,6),5))
+write.table(regions, file="regions.txt", row.names = F, quote=F, sep="\t")
+# Write all the Z files
+k <- 1
+for (j in 1:6) {
+for (chrnum in 1:5) {
+ind <- grep(sprintf("chr%i", chrnum), rsid)
+tmp <- data.frame(rsid = rsid[ind],
+position = pos[ind],
+refAllele=ref,
+altAllele=alt,
+Z=unname(BIGZ[ind, j]))
+write.table(na.omit(tmp), file = filenames[k], quote=FALSE, row.names = FALSE, sep="\t")
+k <- k+1
+}
+}
+# Compute the summary statistic
+setwd("~/tmpdatatest/test2/")
+## There 6 phenotypes
+sumtab <- read.table("summary.txt", sep="\t", header=TRUE, stringsAsFactors = FALSE)
+## Zscore ID: z_CONSORITUM_PHENOTYPE_chr#chr.txt
+ids <- sprintf("z_%s_%s",sumtab$Consortium, sumtab$Outcome)
+## The covariance is set to 1 and the variance to 2
+COV <- toeplitz(c(2,1,1,1,1,1))
+rownames(COV) <- colnames(COV) <- ids
+## Structure:
+# - 5 chromosomes, 2 regions per chromosomes
+# - 10 regions, 2 regions per chromosome
+# - 30 SNPs, 3 SNPs per region
+## Structure of missing values region per region ;
+## ".." means no missing values
+## "XX" means the whole region is missing
+#
+# Z1 Z2 Z3 Z4 Z5 Z6
+# R1 .. .. .. .. .. ..
+# R2 .. .. .. .. .. ..
+# R3 XX .. .. .. .. ..
+# R4 .. XX .. .. .. ..
+# R5 .. .. XX .. .. ..
+# R6 .. .. .. XX .. ..
+# R7 .. .. .. .. XX ..
+# R8 .. .. .. .. .. XX
+# R9 XX XX XX .. .. ..
+# R10 .. .. .. XX XX XX
+filenames <- paste0("~/tmpdatatest/test2/zfiles/", rep(ids,e=5), "_chr", rep(1:5, 6), ".txt")
+## rsid : rs_#chr_#region_#snp
+rsid <- paste0("rs", "_chr", rep(1:5, e=6), # chr
+"_reg", sprintf("%02i", rep(1:10, e=3)), # region
+"_", sprintf("%02i", 1:30)) # snp
+pos <- rep(1:6, 5)
+chr <- rep(1:5, e=6)
+reg <- rep(1:10, e=3)
+ref <- "A"
+alt <- "G"
+BIGZ <- matrix(1:(30*6), 30, 6)
+BIGZ[grep("reg03", rsid),1] <- NA
+BIGZ[grep("reg04", rsid),2] <- NA
+BIGZ[grep("reg05", rsid),3] <- NA
+BIGZ[grep("reg06", rsid),4] <- NA
+BIGZ[grep("reg07", rsid),5] <- NA
+BIGZ[grep("reg08", rsid),6] <- NA
+BIGZ[grep("reg09", rsid),1:3] <- NA
+BIGZ[grep("reg10", rsid),4:6] <- NA
+rownames(BIGZ) <- rsid
+# What does it look like ?
+require(pheatmap)
+png("zscores.png", res = 100)
+pheatmap(BIGZ, cluster_rows = FALSE, cluster_cols = FALSE, cellwidth = 10, cellheight = 10)
+dev.off()
+# Create regions
+# Create Z scores
+# Write covariance matrix
+write.table(data.frame(ID=ids, COV), file="COV.txt", row.names = F, quote=F, sep="\t")
+# Write region file
+regions <- data.frame(chr=sprintf("chr%i", rep(1:5,e=2)),
+start=rep(c(1,4),5),
+stop=rep(c(3,6),5))
+write.table(regions, file="regions.txt", row.names = F, quote=F, sep="\t")
+# Write all the Z files
+k <- 1
+for (j in 1:6) {
+for (chrnum in 1:5) {
+ind <- grep(sprintf("chr%i", chrnum), rsid)
+tmp <- data.frame(rsid = rsid[ind],
+position = pos[ind],
+refAllele=ref,
+altAllele=alt,
+Z=unname(BIGZ[ind, j]))
+write.table(na.omit(tmp), file = filenames[k], quote=FALSE, row.names = FALSE, sep="\t")
+k <- k+1
+}
+}
+# Compute the summary statistic
+write.table(matrix(1:4,2,2))
+write.table(round(matrix(1:4,2,2),2)
+)
+setwd("~/tmpdatatest/test2/")
+## There 6 phenotypes
+sumtab <- read.table("summary.txt", sep="\t", header=TRUE, stringsAsFactors = FALSE)
+## Zscore ID: z_CONSORITUM_PHENOTYPE_chr#chr.txt
+ids <- sprintf("z_%s_%s",sumtab$Consortium, sumtab$Outcome)
+## The covariance is set to 1 and the variance to 2
+COV <- toeplitz(c(2,1,1,1,1,1))
+rownames(COV) <- colnames(COV) <- ids
+## Structure:
+# - 5 chromosomes, 2 regions per chromosomes
+# - 10 regions, 2 regions per chromosome
+# - 30 SNPs, 3 SNPs per region
+## Structure of missing values region per region ;
+## ".." means no missing values
+## "XX" means the whole region is missing
+#
+# Z1 Z2 Z3 Z4 Z5 Z6
+# R1 .. .. .. .. .. ..
+# R2 .. .. .. .. .. ..
+# R3 XX .. .. .. .. ..
+# R4 .. XX .. .. .. ..
+# R5 .. .. XX .. .. ..
+# R6 .. .. .. XX .. ..
+# R7 .. .. .. .. XX ..
+# R8 .. .. .. .. .. XX
+# R9 XX XX XX .. .. ..
+# R10 .. .. .. XX XX XX
+filenames <- paste0("~/tmpdatatest/test2/zfiles/", rep(ids,e=5), "_chr", rep(1:5, 6), ".txt")
+## rsid : rs_#chr_#region_#snp
+rsid <- paste0("rs", "_chr", rep(1:5, e=6), # chr
+"_reg", sprintf("%02i", rep(1:10, e=3)), # region
+"_", sprintf("%02i", 1:30)) # snp
+pos <- rep(1:6, 5)
+chr <- rep(1:5, e=6)
+reg <- rep(1:10, e=3)
+ref <- "A"
+alt <- "G"
+BIGZ <- matrix(1:(30*6), 30, 6) + 0.001
+BIGZ[grep("reg03", rsid),1] <- NA
+BIGZ[grep("reg04", rsid),2] <- NA
+BIGZ[grep("reg05", rsid),3] <- NA
+BIGZ[grep("reg06", rsid),4] <- NA
+BIGZ[grep("reg07", rsid),5] <- NA
+BIGZ[grep("reg08", rsid),6] <- NA
+BIGZ[grep("reg09", rsid),1:3] <- NA
+BIGZ[grep("reg10", rsid),4:6] <- NA
+rownames(BIGZ) <- rsid
+# What does it look like ?
+require(pheatmap)
+png("zscores.png", res = 100)
+pheatmap(BIGZ, cluster_rows = FALSE, cluster_cols = FALSE, cellwidth = 10, cellheight = 10)
+dev.off()
+# Create regions
+# Create Z scores
+# Write covariance matrix
+write.table(data.frame(ID=ids, COV), file="COV.txt", row.names = F, quote=F, sep="\t")
+# Write region file
+regions <- data.frame(chr=sprintf("chr%i", rep(1:5,e=2)),
+start=rep(c(1,4),5),
+stop=rep(c(3,6),5))
+write.table(regions, file="regions.txt", row.names = F, quote=F, sep="\t")
+# Write all the Z files
+k <- 1
+for (j in 1:6) {
+for (chrnum in 1:5) {
+ind <- grep(sprintf("chr%i", chrnum), rsid)
+tmp <- data.frame(rsid = rsid[ind],
+position = pos[ind],
+refAllele=ref,
+altAllele=alt,
+Z=unname(BIGZ[ind, j]))
+write.table(na.omit(tmp), file = filenames[k], quote=FALSE, row.names = FALSE, sep="\t")
+k <- k+1
+}
+}
+# Compute the summary statistic
+rm(list=ls())
+gc()
+data(sleep)
+sleep
+a = data(sleep)
+a
+source('http://www.bioconductor.org/biocLite.R')
+biocLite("pathview")
+# Chargement de la library pathview
+library(pathview)
+# Lecture du tableau
+genesTable <- read.table("data_ps1/genes.txt", sep="\t", header=TRUE)
+# Lecture du tableau
+genesTable <- read.table("data_ps1/genes.txt", sep="\t", header=TRUE)
+setwd("/Volumes/@hubbioit-1/Enseignement/CoursPhD/2018-1-Winter/Practical Session 1")
+# Chargement de la library pathview
+library(pathview)
+# Lecture du tableau
+genesTable <- read.table("data_ps1/genes.txt", sep="\t", header=TRUE)
+genesTable
+# extraire uniquement les noms de genes
+genes <- genes[,1]
+# vérifier la classe de l'objet gene
+class(genes)
+# Lecture du tableau
+genesTable <- read.table("data_ps1/genes.txt", sep="\t", header=TRUE)
+# extraire uniquement les noms de genes
+genes <- genesTable[,1]
+genes
+# vérifier la classe de l'objet gene
+class(genes)
+# la doc de la fonction pathview indique que l'objet genes doit etre un VECTEUR
+genes = as.vector(genes)
+# Choisir son pathway et le type d'annotation de gene
+pathwayID = "hsa04110"
+geneIDTYPE = "SYMBOL"
+# pathview prend en entrée un vecteur ou une matrice gene.data
+pathview(gene.data=genes, pathway.id=pathwayID, gene.idtype=geneIDTYPE, plot.col.key=FALSE)
+genesTable <- read.table("data_ps1/myGenes.csv", sep=";", header=TRUE)
+print(genesTable)
+class(genesTable)
+dim(genesTable)
+genes <- as.vector(genesTable[,2])
+pathwayID <- "hsa04012"
+geneIDTYPE <- "SYMBOL"
+pathview(genes, pathway.id = pathwayID, gene.idtype = geneIDTYPE, plot.col.key= FALSE)
+genesTable <- read.table("data_ps1/myGenes.csv", sep=";", header=TRUE)
+print(genesTable)
+class(genesTable)
+dim(genesTable)
+genes <- as.vector(genesTable[,2])
+pathwayID <- "hsa04012"
+geneIDTYPE <- "SYMBOL"
+pathview(genes, pathway.id = pathwayID, gene.idtype = geneIDTYPE, plot.col.key= FALSE)
+variants <- read.table("data_ps1/VariantsTable.csv", sep="\t", header=TRUE)
+vec1 <- which(variants$ExonicFunc.refGene == "nonsynonymous SNV" |
+variants$ExonicFunc.refGene == "stopgain" |
+variants$ExonicFunc.refGene == "stoploss")
+vec2 <- which(variants$CADD_phred > 12.37)
+vec3 <- intersect(vec1, vec2)
+tab <- variants[vec3,]
+write.table(tab, file="outputTable.txt", sep="t", quote=FALSE, row.names=FALSE)
+View(tab)
+write.table(tab, file="outputTable.txt", sep="\t", quote=FALSE, row.names=FALSE)
+seqs = c('ATGGATTTTATTTAG', 'ATGGATTTTCGC', 'CTACATGGATTTTGAAT', 'aaTGCTAAACtAA', 'TCGATTAA')
+nchar(seqs)
+grep('ATG', seqs, ignore.case = T)
+grep('TGA|TAA|TAG', seqs, ignore.case = T)
+grep('ATG.*TGA|ATG.*TAA|ATG.*TAG', seqs, ignore.case = T)
+require(microbenchmark)
+M <- matrix(1, 10, 10)
+require(microbenchmark)
+M <- matrix(1, 10, 10)
+f1 <- function(M) {
+res <- rep(NA, nrow(M))
+for (i in 1:nrow(M)) res[i] <- sum(M[,i])
+return(sum(res))
+}
+f2 <- function(M) {
+N <- nrow(M)
+res <- rep(NA, N)
+for (i in 1:N) res[i] <- sum(M[,i])
+return(sum(res))
+}
+f3 <- function(M) sum(apply(M, 1, sum)))
+f4 <- function(M) sum(rowSums(M)))
+f3 <- function(M) sum(apply(M, 1, sum))
+f4 <- function(M) sum(rowSums(M))
+?microbenchmark
+res <- microbenchmark(f1(M), f2(M), f3(M), f4(M))
+res <- microbenchmark(f1(M), f2(M), f3(M), f4(M), times=1000000L)
+res <- microbenchmark(f1(M), f2(M), f3(M), f4(M), times=100000L)
+res <- microbenchmark(f1(M), f2(M), f3(M), f4(M), times=1000L)
+plot(res)
+res <- microbenchmark(f1(M), f2(M), f4(M), times=1000L)
+plot(res)
+res <- microbenchmark(f1(M), f2(M), times=1000L)
+plot(res)
+require(ggplot2)
+M <- matrix(1, 10, 10)
+f1 <- function(M) {
+res <- rep(NA, nrow(M))
+for (i in 1:nrow(M)) res[i] <- sum(M[,i])
+return(sum(res))
+}
+f2 <- function(M) {
+N <- nrow(M)
+res <- rep(NA, N)
+for (i in 1:N) res[i] <- sum(M[,i])
+return(sum(res))
+}
+f3 <- function(M) sum(apply(M, 1, sum))
+f4 <- function(M) sum(rowSums(M))
+res <- microbenchmark(f1(M), f2(M), times=1000L)
+plot(res)
+res <- microbenchmark(f1(M), f2(M), times=1000L)
+plot(res)
+M <- matrix(1, 1000, 1000)
+f1 <- function(M) {
+res <- rep(NA, nrow(M))
+for (i in 1:nrow(M)) res[i] <- sum(M[,i])
+return(sum(res))
+}
+f2 <- function(M) {
+N <- nrow(M)
+res <- rep(NA, N)
+for (i in 1:N) res[i] <- sum(M[,i])
+return(sum(res))
+}
+f3 <- function(M) sum(apply(M, 1, sum))
+f4 <- function(M) sum(rowSums(M))
+res <- microbenchmark(f1(M), f2(M), times=1000L)
+M <- matrix(1, 100, 100)
+f1 <- function(M) {
+res <- rep(NA, nrow(M))
+for (i in 1:nrow(M)) res[i] <- sum(M[,i])
+return(sum(res))
+}
+f2 <- function(M) {
+N <- nrow(M)
+res <- rep(NA, N)
+for (i in 1:N) res[i] <- sum(M[,i])
+return(sum(res))
+}
+f3 <- function(M) sum(apply(M, 1, sum))
+f4 <- function(M) sum(rowSums(M))
+res <- microbenchmark(f1(M), f2(M), f3(M), times=1000L)
+plot(res)
+res <- microbenchmark(f1(M), f2(M), f3(M), f4(M), times=1000L)
+plot(res)
+res <- microbenchmark(f1(M), f2(M), f3(M), f4(M), times=1000L)
+plot(res)
+Melanoma
+require(MASS)
+Melanoma
+ChickWeight
+180/5
+"Bonjour"
+plot(1:10)
+plot(1:10, main="c'est trop cool !")
+combin <- function(n=2, k=1){
+maxi <- max(k, n-k)
+mini <- min(k, n-k)
+res <- prod((maxi+1):n) / factorial(mini)
+}
+combin(4, 2)
+combin(4, 2)
+(combin(4, 2))
+(combin(7, 5))
+(combin(7, 3))
+Y <- c(13.86,16.82,13.65,16.53,15.66,16.16,18.05,14.93,16.57,16.54,14.22,14.44,16.95,15.62,15.68,13.62,16.02,17.55,
+13.16,15.75,16.20,14.53,16.84,15.82,16.22,16.79,12.21,16.82,12.22,15.77,15.60,15.87,17.12,15.63,14.92,11.84,
+11.03,12.29,12.35,12.19,12.76,11.83,13.78,14.95,11.25,14.75,15.40,14.54,13.87,14.60,12.40,14.42,14.00,15.91,
+15.83,13.15,15.33,16.55,13.44,14.01,14.80,16.36,15.50,14.30,16.79,16.65,13.86,16.05,16.35,14.05,16.63,14.85,
+13.90,16.70,16.35,16.25,13.89,17.20,14.25,15.69,17.30,17.00,16.85,17.61,16.93,17.20,16.84,17.33,16.68,17.13,
+16.61,16.85,16.23,17.10,17.72,15.65,16.85,16.33,16.95)
+X1 <- c(14.8,31.7,13.7,29.2,19.8,27.2,40.8,24.2,28.3,32.6,16.6,15.7,34.5,21.8,22.2,13.6,24.7,37.0,11.3,23.3,27.3,18.4,
+31.9,23.1,27.8,31.6,18.3,30.0,13.7,23.1,21.8,27.1,33.8,22.0,17.8,11.7,8.9 ,14.2,17.1,22.9,17.3,10.9,20.2,24.0,
+9.0 ,23.3,25.0,18.7,23.1,18.0,11.1,15.1,13.6,25.7,28.2,12.0,23.0,28.3,12.7,15.6,19.0,28.7,21.5,17.5,28.6,33.0,
+14.8,27.0,33.0,16.0,30.5,19.0,15.0,29.8,32.0,32.0,14.2,34.8,17.0,23.8,35.0,33.0,32.0,38.7,35.0,35.0,29.9,35.2,
+31.0,34.0,29.9,32.0,28.0,33.3,37.8,25.0,37.0,29.5,35.0)
+X2 <- c(2.0,0.7,1.0,1.6,1.2,0.7,0.1,1.7,1.2,0.5,0.7,4.3,0.5,1.5,2.0,1.1,1.3,0.4,1.7,0.7,0.3,1.4,0.7,1.9,1.0,0.5,3.9,0.6,
+5.2,1.1,2.0,1.3,0.4,0.6,1.5,5.9,5.7,5.7,4.9,4.4,4.1,4.1,3.7,3.0,2.8,2.8,2.7,2.7,2.5,2.5,2.3,2.0,1.9,1.7,1.4,1.3,
+1.2,1.2,1.2,1.0,1.0,0.9,0.9,0.9,0.9,0.9,0.9,0.8,0.8,0.8,0.8,0.7,0.7,0.6,0.6,0.6,0.6,0.5,0.5,0.5,0.5,0.5,0.4,0.4,
+0.4,0.4,0.4,0.4,0.4,0.4,0.3,0.3,0.3,0.3,0.3,0.3,0.2,0.2,0.1)
+dataset <- data.frame(Y, X1, X2)
+#dataset
+regmodel_1=lm(Y~ X1 + X2)
+b1_hat = summary(regmodel_1)$coefficients[2]
+paste0("b1_hat : ", b1_hat)
+# ------------------------
+regmodel_2=lm(X1 ~ X2)
+ui=regmodel_2$residuals
+regmodel_3=lm(Y~ui)
+g1_hat = summary(regmodel_3)$coefficients[2]
+paste0("g1_hat : ", g1_hat)
+# --------------------------
+regmodel_4=lm(Y ~ X2)
+wi=regmodel_4$residuals
+regmodel_5=lm(wi~ui)
+d1_hat = summary(regmodel_5)$coefficients[2]
+paste0("d1_hat : ", d1_hat)
+# --------------------------
+new_set = subset(dataset, X2 > 2.2)
+regmodel_6=lm(Y~X1 + X2, data=new_set)
+summary(regmodel_6)
+??golub
+table(golub.cl)
+data(golub)
+require(multtest)
+table(golub.cl)
+data(golub)
+table(golub.cl)
+read.table("http://bit.ly/2BIEgiY
+")
+read.table("http://bit.ly/2BIEgiY")
+read.delim("http://bit.ly/2BIEgiY")
+data_exemple = matrix(rnorm(100),ncol=5)
+data_exemple2 = matrix(rnorm(50),ncol=5)
+heatmap.2(data_exemple,
+cexRow=0.5,
+symm=F,symkey=F,symbreaks=T,
+notecol="black", # change font color of cell labels to blacklegend
+margins =c(12,9), # widens margins around plot
+denscol=1,
+tracecol=1,
+density.info="none", # turns off density plot inside color legend
+trace="none", # turns off trace lines inside the heat map
+Colv=FALSE,
+dendrogram ="none"
+)
+library(heatmap.2)
+??heatmap.2
+require(gplots)
+data_exemple = matrix(rnorm(100),ncol=5)
+data_exemple2 = matrix(rnorm(50),ncol=5)
+heatmap.2(data_exemple,
+cexRow=0.5,
+symm=F,symkey=F,symbreaks=T,
+notecol="black", # change font color of cell labels to blacklegend
+margins =c(12,9), # widens margins around plot
+denscol=1,
+tracecol=1,
+density.info="none", # turns off density plot inside color legend
+trace="none", # turns off trace lines inside the heat map
+Colv=FALSE,
+dendrogram ="none"
+)
+heatmap.2(data_exemple2,
+cexRow=0.5,
+symm=F,symkey=F,symbreaks=T,
+notecol="black", # change font color of cell labels to blacklegend
+margins =c(12,9), # widens margins around plot
+denscol=1,
+tracecol=1,
+density.info="none", # turns off density plot inside color legend
+trace="none", # turns off trace lines inside the heat map
+Colv=FALSE,
+dendrogram ="none"
+)
+heatmap.2(data_exemple,
+cexRow=0.5,
+symm=F,symkey=F,symbreaks=T,
+notecol="black", # change font color of cell labels to blacklegend
+margins =c(12,9), # widens margins around plot
+denscol=1,
+tracecol=1,
+density.info="none", # turns off density plot inside color legend
+trace="none", # turns off trace lines inside the heat map
+Colv=FALSE,
+dendrogram ="none"
+)
+heatmap.2(data_exemple,
+cexRow=0.5,
+symm=F,symkey=F,symbreaks=T,
+notecol="black", # change font color of cell labels to blacklegend
+margins =c(12,9), # widens margins around plot
+denscol=1,
+tracecol=1,
+density.info="none", # turns off density plot inside color legend
+trace="none", # turns off trace lines inside the heat map
+Colv=FALSE,
+dendrogram ="none"
+)
+heatmap.2(data_exemple2,
+cexRow=0.5,
+symm=F,symkey=F,symbreaks=T,
+notecol="black", # change font color of cell labels to blacklegend
+margins =c(12,9), # widens margins around plot
+denscol=1,
+tracecol=1,
+density.info="none", # turns off density plot inside color legend
+trace="none", # turns off trace lines inside the heat map
+Colv=FALSE,
+dendrogram ="none"
+)
+pheatmap(data_exemple, cluster_rows = FALSE, cluster_cols = FALSE, cellwidth = 5, cellheight = 5)
+require(pheatmap)
+pheatmap(data_exemple, cluster_rows = FALSE, cluster_cols = FALSE, cellwidth = 5, cellheight = 5)
+pheatmap(data_exemple, cluster_rows = FALSE, cluster_cols = FALSE, cellwidth = 5, cellheight = 5)
+pheatmap(data_exemple2, cluster_rows = FALSE, cluster_cols = FALSE, cellwidth = 5, cellheight = 5)
+devtools::install_git("https://gitlab.pasteur.fr/vguillem/saber_report_html.git/template1")
+devtools::install_git("https://gitlab.pasteur.fr/vguillem/saber_report_html.git/template1")
+devtools::install_git("https://gitlab.pasteur.fr/vguillem/saber_report_html.git/template1")
+install_git("https://gitlab.pasteur.fr/vguillem/saber_report_html.git/template1", credentials = git2r::cred_user_pass("vguillem", getPass::getPass()))
+library(devtools)
+install_git("https://gitlab.pasteur.fr/vguillem/saber_report_html.git/template1", credentials = git2r::cred_user_pass("vguillem", getPass::getPass()))
+install_git("git@gitlab.pasteur.fr:vguillem/saber_report_html.git/template1", credentials = git2r::cred_user_pass("vguillem", getPass::getPass()))
+install_git("git@gitlab.pasteur.fr:vguillem/saber_report_html.git/template1", credentials = git2r::cred_user_pass("vguillem@pasteur.fr", getPass::getPass()))
+install_git("git@gitlab.pasteur.fr:vguillem/saber_report_html.git/template1")
+install_git("git@gitlab.pasteur.fr:vguillem/saber_report_html.git")
+install_git("git@gitlab.pasteur.fr:vguillem/saber_report_html.git", credentials = git2r::cred_user_pass("vguillem", getPass::getPass()))
+install_git("https://gitlab.pasteur.fr/vguillem/saber_report_html.git", credentials = git2r::cred_user_pass("vguillem", getPass::getPass()))
+install_git("https://gitlab.pasteur.fr/vguillem/template1.git", credentials = git2r::cred_user_pass("vguillem", getPass::getPass()))
+install_git("https://gitlab.pasteur.fr/vguillem/template1.git")
+df <- data.frame(x= runif(100, 0, 4*pi))
+df$y <- with(df, x**2 + 10 * sin(x) + rnorm(100))
+ggplot(df, aes(x=x, y=y)) + geom_point() + geom_smooth()
+library(ggplot2)
+ggplot(df, aes(x=x, y=y)) + geom_point() + geom_smooth()
+df <- data.frame(x= runif(100, 0, 4*pi))
+df$y <- with(df, x**2 + 10 * sin(x) + 5 * rnorm(100))
+ggplot(df, aes(x=x, y=y)) + geom_point() + geom_smooth()
+setwd("~/git/template1/inst/rmarkdown/templates/reportbis/skeleton")
+devtools::install("../../../../../../template1/")
diff --git a/inst/rmarkdown/templates/reportbis/skeleton/nips_2017.sty b/inst/rmarkdown/templates/reportbis/skeleton/nips_2017.sty
new file mode 100644
index 0000000000000000000000000000000000000000..506bf23f1ba22d23f9d1280652187f0a40a14eda
--- /dev/null
+++ b/inst/rmarkdown/templates/reportbis/skeleton/nips_2017.sty
@@ -0,0 +1,338 @@
+% partial rewrite of the LaTeX2e package for submissions to the
+% Conference on Neural Information Processing Systems (NIPS):
+%
+% - uses more LaTeX conventions
+% - line numbers at submission time replaced with aligned numbers from
+% lineno package
+% - \nipsfinalcopy replaced with [final] package option
+% - automatically loads times package for authors
+% - loads natbib automatically; this can be suppressed with the
+% [nonatbib] package option
+% - adds foot line to first page identifying the conference
+%
+% Roman Garnett (garnett@wustl.edu) and the many authors of
+% nips15submit_e.sty, including MK and drstrip@sandia
+%
+% last revision: March 2017
+
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{nips_2017}[2017/03/20 NIPS 2017 submission/camera-ready style file]
+
+% declare final option, which creates camera-ready copy
+\newif\if@nipsfinal\@nipsfinalfalse
+\DeclareOption{final}{
+ \@nipsfinaltrue
+}
+
+% declare nonatbib option, which does not load natbib in case of
+% package clash (users can pass options to natbib via
+% \PassOptionsToPackage)
+\newif\if@natbib\@natbibtrue
+\DeclareOption{nonatbib}{
+ \@natbibfalse
+}
+
+\ProcessOptions\relax
+
+% fonts
+\renewcommand{\rmdefault}{ptm}
+\renewcommand{\sfdefault}{phv}
+
+% change this every year for notice string at bottom
+\newcommand{\@nipsordinal}{31st}
+\newcommand{\@nipsyear}{2017}
+\newcommand{\@nipslocation}{Long Beach, CA, USA}
+
+% handle tweaks for camera-ready copy vs. submission copy
+\if@nipsfinal
+ \newcommand{\@noticestring}{%
+ \@nipsordinal\/ Conference on Neural Information Processing Systems
+ (NIPS \@nipsyear), \@nipslocation.%
+ }
+\else
+ \newcommand{\@noticestring}{%
+ Submitted to \@nipsordinal\/ Conference on Neural Information
+ Processing Systems (NIPS \@nipsyear). Do not distribute.%
+ }
+
+ % line numbers for submission
+ \RequirePackage{lineno}
+ \linenumbers
+
+ % fix incompatibilities between lineno and amsmath, if required, by
+ % transparently wrapping linenomath environments around amsmath
+ % environments
+ \AtBeginDocument{%
+ \@ifpackageloaded{amsmath}{%
+ \newcommand*\patchAmsMathEnvironmentForLineno[1]{%
+ \expandafter\let\csname old#1\expandafter\endcsname\csname #1\endcsname
+ \expandafter\let\csname oldend#1\expandafter\endcsname\csname end#1\endcsname
+ \renewenvironment{#1}%
+ {\linenomath\csname old#1\endcsname}%
+ {\csname oldend#1\endcsname\endlinenomath}%
+ }%
+ \newcommand*\patchBothAmsMathEnvironmentsForLineno[1]{%
+ \patchAmsMathEnvironmentForLineno{#1}%
+ \patchAmsMathEnvironmentForLineno{#1*}%
+ }%
+ \patchBothAmsMathEnvironmentsForLineno{equation}%
+ \patchBothAmsMathEnvironmentsForLineno{align}%
+ \patchBothAmsMathEnvironmentsForLineno{flalign}%
+ \patchBothAmsMathEnvironmentsForLineno{alignat}%
+ \patchBothAmsMathEnvironmentsForLineno{gather}%
+ \patchBothAmsMathEnvironmentsForLineno{multline}%
+ }{}
+ }
+\fi
+
+% load natbib unless told otherwise
+\if@natbib
+ \RequirePackage{natbib}
+\fi
+
+% set page geometry
+\usepackage[verbose=true,letterpaper]{geometry}
+\AtBeginDocument{
+ \newgeometry{
+ textheight=9in,
+ textwidth=5.5in,
+ top=1in,
+ headheight=12pt,
+ headsep=25pt,
+ footskip=30pt
+ }
+ \@ifpackageloaded{fullpage}
+ {\PackageWarning{nips_2016}{fullpage package not allowed! Overwriting formatting.}}
+ {}
+}
+
+\widowpenalty=10000
+\clubpenalty=10000
+\flushbottom
+\sloppy
+
+% font sizes with reduced leading
+\renewcommand{\normalsize}{%
+ \@setfontsize\normalsize\@xpt\@xipt
+ \abovedisplayskip 7\p@ \@plus 2\p@ \@minus 5\p@
+ \abovedisplayshortskip \z@ \@plus 3\p@
+ \belowdisplayskip \abovedisplayskip
+ \belowdisplayshortskip 4\p@ \@plus 3\p@ \@minus 3\p@
+}
+\normalsize
+\renewcommand{\small}{%
+ \@setfontsize\small\@ixpt\@xpt
+ \abovedisplayskip 6\p@ \@plus 1.5\p@ \@minus 4\p@
+ \abovedisplayshortskip \z@ \@plus 2\p@
+ \belowdisplayskip \abovedisplayskip
+ \belowdisplayshortskip 3\p@ \@plus 2\p@ \@minus 2\p@
+}
+\renewcommand{\footnotesize}{\@setfontsize\footnotesize\@ixpt\@xpt}
+\renewcommand{\scriptsize}{\@setfontsize\scriptsize\@viipt\@viiipt}
+\renewcommand{\tiny}{\@setfontsize\tiny\@vipt\@viipt}
+\renewcommand{\large}{\@setfontsize\large\@xiipt{14}}
+\renewcommand{\Large}{\@setfontsize\Large\@xivpt{16}}
+\renewcommand{\LARGE}{\@setfontsize\LARGE\@xviipt{20}}
+\renewcommand{\huge}{\@setfontsize\huge\@xxpt{23}}
+\renewcommand{\Huge}{\@setfontsize\Huge\@xxvpt{28}}
+
+% sections with less space
+\providecommand{\section}{}
+\renewcommand{\section}{%
+ \@startsection{section}{1}{\z@}%
+ {-2.0ex \@plus -0.5ex \@minus -0.2ex}%
+ { 1.5ex \@plus 0.3ex \@minus 0.2ex}%
+ {\large\bf\raggedright}%
+}
+\providecommand{\subsection}{}
+\renewcommand{\subsection}{%
+ \@startsection{subsection}{2}{\z@}%
+ {-1.8ex \@plus -0.5ex \@minus -0.2ex}%
+ { 0.8ex \@plus 0.2ex}%
+ {\normalsize\bf\raggedright}%
+}
+\providecommand{\subsubsection}{}
+\renewcommand{\subsubsection}{%
+ \@startsection{subsubsection}{3}{\z@}%
+ {-1.5ex \@plus -0.5ex \@minus -0.2ex}%
+ { 0.5ex \@plus 0.2ex}%
+ {\normalsize\bf\raggedright}%
+}
+\providecommand{\paragraph}{}
+\renewcommand{\paragraph}{%
+ \@startsection{paragraph}{4}{\z@}%
+ {1.5ex \@plus 0.5ex \@minus 0.2ex}%
+ {-1em}%
+ {\normalsize\bf}%
+}
+\providecommand{\subparagraph}{}
+\renewcommand{\subparagraph}{%
+ \@startsection{subparagraph}{5}{\z@}%
+ {1.5ex \@plus 0.5ex \@minus 0.2ex}%
+ {-1em}%
+ {\normalsize\bf}%
+}
+\providecommand{\subsubsubsection}{}
+\renewcommand{\subsubsubsection}{%
+ \vskip5pt{\noindent\normalsize\rm\raggedright}%
+}
+
+% float placement
+\renewcommand{\topfraction }{0.85}
+\renewcommand{\bottomfraction }{0.4}
+\renewcommand{\textfraction }{0.1}
+\renewcommand{\floatpagefraction}{0.7}
+
+\newlength{\@nipsabovecaptionskip}\setlength{\@nipsabovecaptionskip}{7\p@}
+\newlength{\@nipsbelowcaptionskip}\setlength{\@nipsbelowcaptionskip}{\z@}
+
+\setlength{\abovecaptionskip}{\@nipsabovecaptionskip}
+\setlength{\belowcaptionskip}{\@nipsbelowcaptionskip}
+
+% swap above/belowcaptionskip lengths for tables
+\renewenvironment{table}
+ {\setlength{\abovecaptionskip}{\@nipsbelowcaptionskip}%
+ \setlength{\belowcaptionskip}{\@nipsabovecaptionskip}%
+ \@float{table}}
+ {\end@float}
+
+% footnote formatting
+\setlength{\footnotesep }{6.65\p@}
+\setlength{\skip\footins}{9\p@ \@plus 4\p@ \@minus 2\p@}
+\renewcommand{\footnoterule}{\kern-3\p@ \hrule width 12pc \kern 2.6\p@}
+\setcounter{footnote}{0}
+
+% paragraph formatting
+\setlength{\parindent}{\z@}
+\setlength{\parskip }{5.5\p@}
+
+% list formatting
+\setlength{\topsep }{4\p@ \@plus 1\p@ \@minus 2\p@}
+\setlength{\partopsep }{1\p@ \@plus 0.5\p@ \@minus 0.5\p@}
+\setlength{\itemsep }{2\p@ \@plus 1\p@ \@minus 0.5\p@}
+\setlength{\parsep }{2\p@ \@plus 1\p@ \@minus 0.5\p@}
+\setlength{\leftmargin }{3pc}
+\setlength{\leftmargini }{\leftmargin}
+\setlength{\leftmarginii }{2em}
+\setlength{\leftmarginiii}{1.5em}
+\setlength{\leftmarginiv }{1.0em}
+\setlength{\leftmarginv }{0.5em}
+\def\@listi {\leftmargin\leftmargini}
+\def\@listii {\leftmargin\leftmarginii
+ \labelwidth\leftmarginii
+ \advance\labelwidth-\labelsep
+ \topsep 2\p@ \@plus 1\p@ \@minus 0.5\p@
+ \parsep 1\p@ \@plus 0.5\p@ \@minus 0.5\p@
+ \itemsep \parsep}
+\def\@listiii{\leftmargin\leftmarginiii
+ \labelwidth\leftmarginiii
+ \advance\labelwidth-\labelsep
+ \topsep 1\p@ \@plus 0.5\p@ \@minus 0.5\p@
+ \parsep \z@
+ \partopsep 0.5\p@ \@plus 0\p@ \@minus 0.5\p@
+ \itemsep \topsep}
+\def\@listiv {\leftmargin\leftmarginiv
+ \labelwidth\leftmarginiv
+ \advance\labelwidth-\labelsep}
+\def\@listv {\leftmargin\leftmarginv
+ \labelwidth\leftmarginv
+ \advance\labelwidth-\labelsep}
+\def\@listvi {\leftmargin\leftmarginvi
+ \labelwidth\leftmarginvi
+ \advance\labelwidth-\labelsep}
+
+% create title
+\providecommand{\maketitle}{}
+\renewcommand{\maketitle}{%
+ \par
+ \begingroup
+ \renewcommand{\thefootnote}{\fnsymbol{footnote}}
+ % for perfect author name centering
+ \renewcommand{\@makefnmark}{\hbox to \z@{$^{\@thefnmark}$\hss}}
+ % The footnote-mark was overlapping the footnote-text,
+ % added the following to fix this problem (MK)
+ \long\def\@makefntext##1{%
+ \parindent 1em\noindent
+ \hbox to 1.8em{\hss $\m@th ^{\@thefnmark}$}##1
+ }
+ \thispagestyle{empty}
+ \@maketitle
+ \@thanks
+ \@notice
+ \endgroup
+ \let\maketitle\relax
+ \let\thanks\relax
+}
+
+% rules for title box at top of first page
+\newcommand{\@toptitlebar}{
+ \hrule height 4\p@
+ \vskip 0.25in
+ \vskip -\parskip%
+}
+\newcommand{\@bottomtitlebar}{
+ \vskip 0.29in
+ \vskip -\parskip
+ \hrule height 1\p@
+ \vskip 0.09in%
+}
+
+% create title (includes both anonymized and non-anonymized versions)
+\providecommand{\@maketitle}{}
+\renewcommand{\@maketitle}{%
+ \vbox{%
+ \hsize\textwidth
+ \linewidth\hsize
+ \vskip 0.1in
+ \@toptitlebar
+ \centering
+ {\LARGE\bf \@title\par}
+ \@bottomtitlebar
+ \if@nipsfinal
+ \def\And{%
+ \end{tabular}\hfil\linebreak[0]\hfil%
+ \begin{tabular}[t]{c}\bf\rule{\z@}{24\p@}\ignorespaces%
+ }
+ \def\AND{%
+ \end{tabular}\hfil\linebreak[4]\hfil%
+ \begin{tabular}[t]{c}\bf\rule{\z@}{24\p@}\ignorespaces%
+ }
+ \begin{tabular}[t]{c}\bf\rule{\z@}{24\p@}\@author\end{tabular}%
+ \else
+ \begin{tabular}[t]{c}\bf\rule{\z@}{24\p@}
+ Anonymous Author(s) \\
+ Affiliation \\
+ Address \\
+ \texttt{email} \\
+ \end{tabular}%
+ \fi
+ \vskip 0.3in \@minus 0.1in
+ }
+}
+
+% add conference notice to bottom of first page
+\newcommand{\ftype@noticebox}{8}
+\newcommand{\@notice}{%
+ % give a bit of extra room back to authors on first page
+ \enlargethispage{2\baselineskip}%
+ \@float{noticebox}[b]%
+ \footnotesize\@noticestring%
+ \end@float%
+}
+
+% abstract styling
+\renewenvironment{abstract}%
+{%
+ \vskip 0.075in%
+ \centerline%
+ {\large\bf Abstract}%
+ \vspace{0.5ex}%
+ \begin{quote}%
+}
+{
+ \par%
+ \end{quote}%
+ \vskip 1ex%
+}
+
+\endinput
diff --git a/inst/rmarkdown/templates/reportbis/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/reportbis/skeleton/skeleton.Rmd
new file mode 100644
index 0000000000000000000000000000000000000000..1ec6cdb0cebe80ea9c84f78aab96456450be4325
--- /dev/null
+++ b/inst/rmarkdown/templates/reportbis/skeleton/skeleton.Rmd
@@ -0,0 +1,39 @@
+---
+title: 'This the title'
+author: 'Jean Bon'
+date: ''
+output: pdf_document
+subtitle: ''
+---
+
+```{r setup, include=FALSE, message=FALSE, warning=FALSE}
+knitr::opts_chunk$set(echo = FALSE)
+library(ggplot2)
+```
+
+# 1. Data
+
+# 2. Analysis
+
+Here is how to include the beautiful Fig. \ref{fig:simul} in the report.
+
+```{r simul, fig.cap="The caption", fig.align='center', fig.pos="!h"}
+df <- data.frame(x= runif(100, 0, 4*pi))
+df$y <- with(df, x**2 + 10 * sin(x) + 5 * rnorm(100))
+ggplot(df, aes(x=x, y=y)) + geom_point() + geom_smooth()
+```
+
+
+# 3. Results
+
+\newpage
+
+# Appendix A: R session information
+
+In the reproducible research framework, an important step is to save all the versions of the softwares used to perform the statistical analysis. They must be provided when submitting a paper.
+
+```{r sessionInfo}
+print(sessionInfo(), locale=FALSE)
+```
+
+# Appendix B: References
diff --git a/inst/rmarkdown/templates/reportbis/template.yaml b/inst/rmarkdown/templates/reportbis/template.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..d01441f22150b03aa132116fe254665ff8e5d7c2
--- /dev/null
+++ b/inst/rmarkdown/templates/reportbis/template.yaml
@@ -0,0 +1,4 @@
+name: SABER report PDF
+description: >
+ SABER pdf template for reports
+create_dir: true
\ No newline at end of file