########### produce the output image
png("T:dataforfigshare.png")

layout(matrix(c(1,1,2,3), 2, 2, byrow = TRUE))
#
variables = list (as.factor (data_ordtot$genotype), data_ordtot$ind)
LI_mean <- tapply(data_ordtot$values, variables, mean, na.rm= TRUE)
LI_sem <- tapply(data_ordtot$values, variables, std.error)
samplesize <-as.matrix(summary (data$genotype))

bar <- barplot(LI_mean, beside=T, ylim = c(-0.7,1),  main=("nocolorlearning"),
               axisnames =F, legend.text=(   paste(levels(data$genotype), "(n=",samplesize,")"  )      ), args.legend = list(x = "bottomright", ncol=2) ) 
# store location of bars in bar, and
# plot the barplot. ylim is used to
# make room for the error bar later
arrows(bar, LI_mean + LI_sem, bar, LI_mean - LI_sem,
       length = 0, # width of the arrowhead
       angle = 90, # angle of the arrowhead 
       code = 3 # arrowhead in both ends
)

axis(1, at=seq(bar [2,1], bar [2,7],by= (length(levels(data_ordtot$genotype))+1)), tick =T,
     labels=c("pretest","training","training","test","training","training","test"), las = 1) 
abline(h=seq(0,1,.2),col=2, lty=3)
#
plot(data$X8_test2/10000~data$genotype, las=2, ylab="learning score", xlab="", cex.axis=0.6,main="score absolute during final test")
abline(h=0, col=2)
#
plot(data$scorerelative~data$genotype, las=2, ylab="learning score", xlab="", cex.axis=0.6, main="score final test - pretest")
abline(h=0, col=2)
dev.off()
### write data file
write.csv(data_ori, file="T:data.csv")

#############################################################################################################################
########### on Figshare


## you need to install Rtools first (the version which correspond to your R version)
## install devtools package then, rjson package
# you need to set figshare to receive R commands: https://github.com/ropensci/rfigshare

## Julien Colomb = 97229
## Björn Brembs = 96464

###start installing packages


# colomb account
options(FigshareKey = "jBkrLNsYbeov2oM09cXBBw")
options(FigsharePrivateKey = "LhQkDeJaVJzAhWRIKYeobA")
options(FigshareToken = "BYuYn4OjWjd8njBKCyeFXQOEAYY1MfLJ1Y0z80rVWj6AXYuYn4OjWjd8njXKCyeFXQ")
options(FigsharePrivateToken = "aC2q4lBod3Xl52CeKwp7Fg")
###end figshare info

#brembs lab account
options(FigshareKey = "ABqLKahr9d8EBuBCdBBxpg")
options(FigsharePrivateKey = "OCehduRnbLFvQBtD4KAZBA")
options(FigshareToken = "Jr4eYBQkgEuOvJ5PdAlXpQ851uziewWIa5M3EgqpySAQJr4eYXQkgEuOvJ5PdAlXpQ")
options(FigsharePrivateToken = "0WX9Lz0bWN5TA3fP0xnAXA")
###end figshare info

require(rfigshare)
fs_auth()

##need to create the article and get its id here: do it only once, then write the id and comment this part:

### fileset where all other will be included (not implemented yet)
if (is.na(id_fileset)){
  id <- fs_new_article(title = article_title, description = article_description, 
                       type = "fileset", tags = article_tags, categories=article_categories ,
                       files = "D:/Bilder/Toolbox/fulogo.jpg",
                       visibility= article_visibility, authors = article_authors,
                       links=article_links)
  id_fileset <- id
  
}

### Figure for the experiment: result page
if (is.na(id_figure)){
  id <- fs_new_article(title = paste("figure for",article_title), description = article_description, 
                       type = article_type, tags = article_tags, categories=article_categories ,
                       files = "T:dataforfigshare.png", visibility= article_visibility, authors = article_authors,
                       links=article_links)
    
  id_figure <- id
  
}else{
  newfile= "T:dataforfigshare.png"
  fs_upload(id_figure, file =newfile)
}

### data analyzed for the experiment: data dataset
if (is.na(id_data)){
  id <- fs_new_article(title = paste("data for",article_title), description = "analyzed data. Were excluded from the analysis: <br> data with an entry in the remark field, <br> data with a pretest score >6000.", 
                       type = "dataset", tags = article_tags, categories=article_categories ,
                       files = "T:data.csv", visibility= article_visibility, authors = article_authors,
                       links=article_links)
  id_data <- id

}else{
  newfile= "T:data.csv"
  fs_upload(id_data, file =newfile)
}

### raw data produced during the experiment (no formatting): drawdata dataset
#1 make the article
if (is.na(id_rawdata)){
  id <- fs_new_article(title = paste("raw data for",article_title), description = "raw data, columns are time(ms)-torque measure (V)- phase of the paradigm - laser on signal. note that discrepency between the raw data and the analysed data can be found for pretest phase: the zero is sometimes readjusted at the end of the prephase and the score recalculated.", 
                       type = "fileset", tags = article_tags, categories=article_categories ,
                       #files = list(rawfilenames),
                       visibility= article_visibility, authors = article_authors,
                       links=article_links)
    id_rawdata <- id
  }
#2 upload the files (only the one not already uploaded)
if (length(rawfilenames)>alreadyuploaded){
  first=alreadyuploaded+1
  for (i in c(first:length(rawfilenames))){
    fs_upload(id_rawdata,rawfilenames[i])
    
  }
}

alreadyuploaded <- length(rawfilenames)

if (is.na(id_code)){
  id <- fs_new_article(title = paste("code used for analysing",article_title), description = "code used, two codes are called from the first main file, the address of these code would have to be modified for the code to be run)", 
                       type = "fileset", tags = article_tags, categories=article_categories ,
                       #files = list(rawfilenames),
                       visibility= "public", authors = article_authors,
                       links=article_links)
  id_code <- id
}
#2 upload the files (only the one not already uploaded)
fs_upload(id_code,thisfile)
fs_upload(id_code,"D:/dokumente/data/Rfiles/fs/dataanalysis3g.r")
fs_upload(id_code,"D:/dokumente/data/Rfiles/fs/dataanalysisfigshare.r")




##write info that will be needed for updating the articles

ids <- c("id_fileset"= id_fileset, "id_figure"=id_figure, "id_data"=id_data,"id_rawdata"=id_rawdata, "id_code"=id_code,"alreadyuploaded"=alreadyuploaded)
write.table(ids, file="id_numbers.txt")


#


# 
# tests
# 
# fs_update
#    article_title= "test3"
#   article_description = "this is a temporary article"
#   article_type =  "figure"   #, "dataset" #,"media", "poster", "paper", "fileset"
#   article_tags = c("self-learning","genetics")
#   article_categories="Neuroscience"
#   article_files = "T:dataforfigshare.png"
#   article_visibility=   "draft" #"private" "public" #
#   article_authors= list("97229")
# article_authors= list("97229","96612")
#   article_links="http://lab.brembs.net"
# 
# 
# id <- fs_new_article(title = article_title, description = article_description, 
#                      type = article_type, tags = article_tags, categories=article_categories ,
#                      files = article_files, visibility= article_visibility, #authors = article_authors,
#                      links=article_links)
# 
# fs_add_authors(id,article_authors)
# fs_author_search("julien colomb")
# 
# id <- fs_new_article(title="A Test of rfigshare",
#                      description="This is a test of the fs_new_aricle function and related methods"
# ,
#                      type="figure",
#                      authors=c("97306")
#                      ,tags=c("ecology", "openscience"),
#                      categories="Ecology",
#                      links="http://ropensci.org",
#                      files= article_files,
#                     # visibility="private"
#                      )
# 
# id <- fs_new_article(title="A Test of rfigshare",
#                      description="This is a test of the fs_new_aricle function and related methods",
#                      type="figure",
#                      authors=c("97306", "Scott Chamberlain"),
#                      tags=c("ecology", "openscience"),
#                      categories="Ecology",
#                      links="http://ropensci.org",
#                      files="figure/rfigshare.png",
#                      visibility="private")
# fs_delete(id)