Spaces:
Sleeping
Sleeping
File size: 7,790 Bytes
fc8a1cf |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 |
## ======================================================== ##
## 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)
|