########### 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:
data with an entry in the remark field,
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)