alex.waterfall.plot: Prepare Waterfall Plot of Lesion and Expression Data

In GRIN2: Genomic Random Interval (GRIN)

Prepare Waterfall Plot of Lesion and Expression Data

Description

Function return a waterfall plot for expression data by lesion groups of a selected gene.

Usage

alex.waterfall.plot(waterfall.prep, lsn.data, lsn.clrs = NULL, delta = 0.5)

Arguments

waterfall.prep	Output of the alex.waterfall.prep function. It's a list of three data tables that include "gene.lsn.exp" that has patient ID, lesion type that affect this gene if any and expression level of the selected gene, "lsns" which is a data table with all lesions affecting the gene of interest in a GRIN compatible format and "stats" which is one row with the Kruskal-Wallis test result (output of the KW.hit.express function).
lsn.data	Lesion data in a GRIN compatible format.
lsn.clrs	Assigned colors per lesion types. If not specified, colors will be automatically assigned using default.grin.colors function.
delta	Spacing argument for the waterfall plot.

Details

Function return a waterfall plot for expression data by lesion groups of a selected gene. This plot offers a side by side graphical representation of lesion and expression data for each patient where lesion groups are ordered alphabetically. For each lesion category, expression data is ordered from the lowest to the highest with patient with the median expression of the gene in the middle of the panel.

Value

Function return a waterfall plot for expression data by lesion groups of a selected gene.

Author(s)

Abdelrahman Elsayed [e-mail] and Stanley Pounds [e-mail]

References

Cao, X., Elsayed, A. H., & Pounds, S. B. (2023). Statistical Methods Inspired by Challenges in Pediatric Cancer Multi-omics.

See Also

alex.prep.lsn.expr(), KW.hit.express(), alex.waterfall.prep()

Examples

data(expr.data)
data(lesion.data)
data(hg19.gene.annotation)

# prepare expression, lesion data and return the set of genes with both types of data available
# ordered by gene IDs in rows and patient IDs in columns:
alex.data=alex.prep.lsn.expr(expr.data, lesion.data,
                             hg19.gene.annotation, min.expr=1, min.pts.lsn=5)

# run KW test for association between lesion groups and expression level of the same gene:
alex.kw.results=KW.hit.express(alex.data, hg19.gene.annotation, min.grp.size=5)

# To prepare lesion and expression data for a waterfall plot (WT1 gene):
WT1.waterfall.prep=alex.waterfall.prep(alex.data, alex.kw.results, "WT1", lesion.data)

# waterfall plot of WT1 gene:
WT1.waterfall.plot=alex.waterfall.plot(WT1.waterfall.prep, lesion.data)

GRIN2 documentation built on April 4, 2025, 1:41 a.m.