plotCompareScores: Compare two genomic features by score and display them in a...

In AJEinstein/SMITE: Significance-based Modules Integrating the Transcriptome and Epigenome

Description

This function creates a hexbin of the log transformed p-value/score for any two expression or modification-context pairing within a PvalueObject inside of a PvalueAnnotation

Usage

plotCompareScores(pvalue_annotation, x_name, y_name, ...)

Arguments

pvalue_annotation	An S4 object of class PvalueAnnotation for which a PvalueObject has already been created
x_name	A string to be grepped from the columns within the slot "pval_data" that is within the PvalueAnnotation slot "score_data." This column will be plotted on the x-axis with a direction specified from the corresponding effect column.
y_name	A string to be grepped from the columns within the slot "pval_data" that is within the PvalueAnnotation slot "score_data." This column will be plotted on the y-axis with a direction specified from the corresponding effect column.
...	Other plotting parameters

Details

This plotting function creates a hexbin plot of any two p-value vectors stored within a p-value object. It can be used to define relationships between direction and significance in different genomic contexts after having combined p-values.

Value

A hexbin plot

Author(s)

N. Ari Wijetunga

See Also

makePvalueObject plotDensityPval

Examples

data(test_annotation_score_data)

plotCompareScores(pvalue_annotation=test_annotation, x_name="expression", 
y_name="methylation_promoter")

AJEinstein/SMITE documentation built on Oct. 23, 2021, 7:44 a.m.