sraGraph | R Documentation |
This function will create a new graphNEL object from SRA accessions using function of entityGraph
and SRA accessions are returned from SRA full text search using function of getSRA
sraGraph(search_terms, sra_con)
search_terms |
Free text search terms constructed according to SQLite query syntax defined here: http://www.sqlite.org/fts3.html#section_1_3 |
sra_con |
Connection to the SRAmetadb SQLite database |
This function is a wrapper of two functions: acc <- getSRA(search_terms, out_types='sra', sra_con, acc_only=TRUE)
and g <- entityGraph(acc). A graphNEL object with edgemode='directed' is created from input data.frame of SRA accessions and the plot
function will draw a graph
A graphNEL object with edgemode='directed'
Jack Zhu <zhujack@mail.nih.gov> and Sean Davis <sdavis2@mail.nih.gov>
getSRA
, sraConvert
, entityGraph
## Using the SRAmetadb demo database library(SRAdb) library(Rgraphviz) sra_dbname <- file.path(system.file('extdata', package='SRAdb'), 'SRAmetadb_demo.sqlite') sra_con <- dbConnect(dbDriver("SQLite"), sra_dbname) ## create a graphNEL object from SRA accessions, which are full text search results of terms 'primary thyroid cell line' g <- sraGraph('MCF7 OR "MCF-7"', sra_con) attrs <- getDefaultAttrs(list(node=list(fillcolor='lightblue', shape='ellipse'))) plot(g, attrs=attrs) ## similiar search as the above, returned much larger data.frame and graph is too clouded g <- sraGraph('MCF', sra_con) ## Not run: plot(g) ## End(Not run) ## The actual SRAmetadb sqlite database can be downloaded using function: getSRAdbFile. Warning: the actual SRAmetadb sqlite database is pretty large (> 35GB as of May, 2018) after uncompression. So, downloading and uncompressing of the actual SRAmetadb sqlite could take quite a few minutes depending on your network bandwidth. Direct links for downloading the SRAmetadb sqlite database: https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz
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