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| ## ======================================================== ## | |
| ## Menu : Microarray | |
| ## ======================================================== ## | |
| # Loading data #### | |
| load("data/microarray/SRscore_microarray.RData") | |
| colnames_microarray <- colnames(Filter(is.numeric, SRscore_microarray)) | |
| SRscore_microarray[colnames_microarray] <- round(SRscore_microarray[colnames_microarray]) | |
| load("data/microarray/SRratio/ABA.RData") | |
| load("data/microarray/SRratio/cold.RData") | |
| load("data/microarray/SRratio/DC3000.RData") | |
| load("data/microarray/SRratio/drought.RData") | |
| load("data/microarray/SRratio/heat.RData") | |
| load("data/microarray/SRratio/highlight.RData") | |
| load("data/microarray/SRratio/hypoxia.RData") | |
| load("data/microarray/SRratio/osmotic.RData") | |
| load("data/microarray/SRratio/oxidation.RData") | |
| load("data/microarray/SRratio/salt.RData") | |
| load("data/microarray/SRratio/wound.RData") | |
| load("data/microarray/Metadata/ABA.RData") | |
| load("data/microarray/Metadata/cold.RData") | |
| load("data/microarray/Metadata/DC3000.RData") | |
| load("data/microarray/Metadata/drought.RData") | |
| load("data/microarray/Metadata/heat.RData") | |
| load("data/microarray/Metadata/highlight.RData") | |
| load("data/microarray/Metadata/hypoxia.RData") | |
| load("data/microarray/Metadata/osmotic.RData") | |
| load("data/microarray/Metadata/oxidation.RData") | |
| load("data/microarray/Metadata/salt.RData") | |
| load("data/microarray/Metadata/wound.RData") | |
| # Color settings of a heatmap #### | |
| paletteLength <- 100 | |
| microarrayBreaks <- c(seq(min(Filter(is.numeric, SRscore_microarray)), 0, length.out = (paletteLength/2)), | |
| seq(0, max(Filter(is.numeric, SRscore_microarray)), length.out = (paletteLength/2))[-1]) | |
| microarrayColor <- colorRampPalette(c("deepskyblue", "white", "hotpink"))(paletteLength) | |
| # Links to external databases #### | |
| link <- rep("link", nrow(SRscore_microarray)) | |
| ## AlphaFold2 | |
| url <- rep(paste0("https://alphafold.ebi.ac.uk/search/text/", | |
| SRscore_microarray$ensembl_gene_id)) | |
| AF2 <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| ## ATTED-II | |
| url <- rep(paste0("https://atted.jp/kwsearch/?stype=any&kword=", | |
| SRscore_microarray$ensembl_gene_id, | |
| "&searchBtnK.x=0&searchBtnK.y=0")) | |
| ATTED2 <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| ## eFP Browser | |
| url <- rep(paste0("https://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi?dataSource=Abiotic_Stress&mode=Absolute&primaryGene=", | |
| SRscore_microarray$ensembl_gene_id)) | |
| eFP <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| ## KEGG | |
| url <- rep(paste0("https://www.genome.jp/dbget-bin/www_bget?ath:", SRscore_microarray$ensembl_gene_id)) | |
| KEGG <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| ## STRING | |
| url <- rep(paste0("https://string-db.org/cgi/network?identifiers=", | |
| SRscore_microarray$ensembl_gene_id, | |
| "&species=3702&show_query_node_labels=1")) | |
| STRING <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| ## TAIR | |
| url <- rep(paste0("https://www-arabidopsis-org.translate.goog/servlets/TairObject?type=locus&name=", | |
| SRscore_microarray$ensembl_gene_id, | |
| "&_x_tr_sl=en&_x_tr_tl=ja&_x_tr_hl=ja&_x_tr_pto=sc")) | |
| TAIR <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| ## ThaleMine | |
| url <- rep(paste0("https://bar.utoronto.ca/thalemine/keywordSearchResults.do?searchTerm=", | |
| SRscore_microarray$ensembl_gene_id, "&searchSubmit=GO")) | |
| TM <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| ## Joining links to the atlas | |
| SRscore_microarray <- cbind(SRscore_microarray, "AlphaFold2" = AF2, "ATTED-II" = ATTED2, "eFP Browser" = eFP, | |
| "KEGG" = KEGG, "STRING" = STRING, "TAIR" = TAIR, "Thale Mine" = TM) | |
| ## Convert the atlas to template matching format | |
| genefinder_microarray <- column_to_rownames(SRscore_microarray, var = "ensembl_gene_id") | |
| genefinder_microarray <- Filter(is.numeric, genefinder_microarray) | |
| genefinder_microarray <- as.matrix(genefinder_microarray) | |
| ## ========================================================= ## | |
| ## Menu : RNA-Seq | |
| ## ========================================================= ## | |
| # Loading data #### | |
| load("data/rnaseq/SRscore_rnaseq.RData") | |
| colnames_rnaseq <- colnames(Filter(is.numeric, SRscore_rnaseq)) | |
| SRscore_rnaseq[colnames_rnaseq] <- round(SRscore_rnaseq[colnames_rnaseq]) | |
| load("data/rnaseq/SRratio/ABA.RData") | |
| load("data/rnaseq/SRratio/cold.RData") | |
| load("data/rnaseq/SRratio/DC3000.RData") | |
| load("data/rnaseq/SRratio/drought.RData") | |
| load("data/rnaseq/SRratio/heat.RData") | |
| load("data/rnaseq/SRratio/highlight.RData") | |
| load("data/rnaseq/SRratio/hypoxia.RData") | |
| load("data/rnaseq/SRratio/osmotic.RData") | |
| load("data/rnaseq/SRratio/oxidation.RData") | |
| load("data/rnaseq/SRratio/salt.RData") | |
| load("data/rnaseq/SRratio/wound.RData") | |
| load("data/rnaseq/Metadata/ABA.RData") | |
| load("data/rnaseq/Metadata/cold.RData") | |
| load("data/rnaseq/Metadata/DC3000.RData") | |
| load("data/rnaseq/Metadata/drought.RData") | |
| load("data/rnaseq/Metadata/heat.RData") | |
| load("data/rnaseq/Metadata/highlight.RData") | |
| load("data/rnaseq/Metadata/hypoxia.RData") | |
| load("data/rnaseq/Metadata/osmotic.RData") | |
| load("data/rnaseq/Metadata/oxidation.RData") | |
| load("data/rnaseq/Metadata/salt.RData") | |
| load("data/rnaseq/Metadata/wound.RData") | |
| # Color settings of a heatmap #### | |
| paletteLength <- 100 | |
| rnaseqBreaks <- c(seq(min(Filter(is.numeric, SRscore_rnaseq)), 0, length.out = (paletteLength/2)), | |
| seq(0, max(Filter(is.numeric, SRscore_rnaseq)), length.out = (paletteLength/2))[-1]) | |
| rnaseqColor <- colorRampPalette(c("deepskyblue", "white", "hotpink"))(paletteLength) | |
| # Links to external databases #### | |
| link <- rep("link", nrow(SRscore_rnaseq)) | |
| ## AlphaFold2 | |
| url <- rep(paste0("https://alphafold.ebi.ac.uk/search/text/", | |
| SRscore_rnaseq$ensembl_gene_id)) | |
| AF2 <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| ## ATTED-II | |
| url <- rep(paste0("https://atted.jp/kwsearch/?stype=any&kword=", | |
| SRscore_rnaseq$ensembl_gene_id, | |
| "&searchBtnK.x=0&searchBtnK.y=0")) | |
| ATTED2 <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| ## eFP Browser | |
| url <- rep(paste0("https://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi?dataSource=Abiotic_Stress&mode=Absolute&primaryGene=", | |
| SRscore_rnaseq$ensembl_gene_id)) | |
| eFP <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| ## KEGG | |
| url <- rep(paste0("https://www.genome.jp/dbget-bin/www_bget?ath:", SRscore_rnaseq$ensembl_gene_id)) | |
| KEGG <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| ## STRING | |
| url <- rep(paste0("https://string-db.org/cgi/network?identifiers=", | |
| SRscore_rnaseq$ensembl_gene_id, | |
| "&species=3702&show_query_node_labels=1")) | |
| STRING <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| ## TAIR | |
| url <- rep(paste0("https://www-arabidopsis-org.translate.goog/servlets/TairObject?type=locus&name=", | |
| SRscore_rnaseq$ensembl_gene_id, | |
| "&_x_tr_sl=en&_x_tr_tl=ja&_x_tr_hl=ja&_x_tr_pto=sc")) | |
| TAIR <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| ## ThaleMine | |
| url <- rep(paste0("https://bar.utoronto.ca/thalemine/keywordSearchResults.do?searchTerm=", | |
| SRscore_rnaseq$ensembl_gene_id, "&searchSubmit=GO")) | |
| TM <- paste0("<a href = ", "'", url, "'", ">", link, "</a>") | |
| # Joining links to the atlas | |
| SRscore_rnaseq <- cbind(SRscore_rnaseq, "AlphaFold2" = AF2, "ATTED-II" = ATTED2, "eFP Browser" = eFP, | |
| "KEGG" = KEGG, "STRING" = STRING, "TAIR" = TAIR, "Thale Mine" = TM) | |
| # Convert the atlas to template matching format | |
| genefinder_rnaseq <- column_to_rownames(SRscore_rnaseq, var = "ensembl_gene_id") | |
| genefinder_rnaseq <- Filter(is.numeric, genefinder_rnaseq) | |
| genefinder_rnaseq <- as.matrix(genefinder_rnaseq) | |