drawORA: To draw the gene ontology DAG containing ORA results'...

Description Usage Arguments Details Author(s) See Also

Description

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

Usage

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

MarkHeadlines = TRUE, Overwrite = TRUE)

Arguments

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' 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.

Details

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.

Author(s)

CL

See Also

For further details about ORAresults, please see ORA.


CLippmann/dbtORA documentation built on May 26, 2019, 6:40 a.m.