drawORA: To draw the gene ontology DAG containing ORA results'...
In CLippmann/ORA: Overrepresentation Analysis

Description Usage Arguments Details Author(s) See Also

To draw the gene ontology DAG containing ORA results' information. Prepares data for plotGOgraph which does the actual plotting.

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drawORA(ORAresults, PlotFileWithExt, PlotDirectory, MarkDetails = TRUE, 

MarkHeadlines = TRUE, Overwrite = TRUE)

`ORAresults`	List of 4: LRNresults List of 16: Information needed to generate the lrn file containing all the calculated values for the GO terms found to be significant for input genes. NAMESresults List of 3: Information needed to generate the names file containing information about GO terms. Genes2GOtermsSparseMatrix Numeric; Sparse matrix explaining the connection of genes and GO terms. Genes2GOtermsSparseMatrix[i,3]==1 iff gene in ith row is annotated to GO term in ith row. GO2GOAdjMatrices List of 4: Adjacency matrices for each ontology and combined sparse matrix.
`PlotFileWithExt`	String; Name of the file that should be drawn with extension. Extension can be one of 'png', 'eps', 'svg' or 'pdf'. Default is 'png'.
`PlotDirectory`	String; Default: current directory Directory where PlotFileWithExt should be saved.
`MarkDetails`	Boolean; Default: TRUE Set TRUE if details of DAG should be marked in blue colour.
`MarkHeadlines`	Boolean; Default: TRUE Set TRUE if headlines should be marked in yellow colour in DAG.
`Overwrite`	Boolean; Default: TRUE Set TRUE if existing files with the same name should be overwritten.

Coloring of the nodes and its meaning: Significantly overrepresented nodes are marked in red; Significantly underrepresented nodes are marked in green; Terms that are important for DAG structure but do not have a significant p-value are left white. If MarkHeadlines = TRUE, the significant(!) nodes with highest remarkable value in each path from a detail to the root get a yellow filling. The margin indicates over- or underrepesentation by its red or green color. If MarkDetails = TRUE, the details of the DAG will be colored in blue. The margin again indicates over- or underrepesentation by its red or green color. If MarkHeadlines and MarkDetails are TRUE, there might be nodes that are both headlines and details. In this case the nodes have a maring acording to over- or underrepesentation in red or green and are filled in yellow like all headlines. Additionally the writing is blue to indicate that this node is a detail.

For further details about ORAresults, please see ORA.

CLippmann/ORA documentation built on Feb. 4, 2020, 9:38 p.m.