plotHapTable: plotHapTable

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

plotHapTable

Description

display hap result as a table-like figure

Usage

plotHapTable(hapSummary,
             hapPrefix = "H",
             title = "",
             geneName = geneName,
             INFO_tag = NULL,
             tag_split = tag_split,
             tag_field = tag_field,
             tag_name = tag_name,
             displayIndelSize = 0, angle = c(0,45,90),
             replaceMultiAllele = TRUE,
             ALLELE.color = "grey90")

Arguments

hapSummary	object of hapSummary class
hapPrefix	prefix of haplotype names. Default as "H"
title	the main title of the final figure
geneName	character, will be used for filter INFO filed of ANN
INFO_tag	The annotations in the INFO field are represented as tag-value pairs, where the tag and value are separated by an equal sign, ie "=", and pairs are separated by colons, ie ";". For more information please see details.
tag_split	usually, the value of tag-value contains one information. However, if a tag contains more than one fields, eg "ANN", then tag_split is needed. When INFO_tag was set as "ANN" or "SNPEFF", tag_split will be set as "|" by default, see details.
tag_field	integer, if a tag-value contains more than one fields, user need to specified which field should be display. If tag_field set as 0, the whole contents will be displayed. Default as 0.
tag_name	tag name is displayed in Hap figure. If tag_name is missing, will take the value of INFO_tag.
displayIndelSize	display indels with max size of displayIndelSize, If set as 0, all indels will convert into "i*" of which "i" represents "indel".
angle	the angle of coordinates, should be one of 0, 45 and 90
replaceMultiAllele	whether to replace MultiAllele with "T*", default as TRUE.
ALLELE.color	the color of ALLELE row, default as "grey90"

Details

In VCF files, the INFO field are represented as tag-value pairs, where the tag and value are separated by an equal sign, ie "=", and pairs are separated by colons, ie ";".

If hapSummarys were generated from sequences, INFO row is null. If hapSummarys were generated from VCF, INFO was take from the INFO column in the source VCF file. Some tag-values may contains more than one value separated by "|", eg.: "ANN" or "snpEFF" added by 'snpeff' or other software. For those fields we need specified value of tag_field = "ANN" and tag_split = "[\|]", it's suggest specified the value of tag_name for display in figure.

'snpeff', a toolbox for genetic variant annotation and functional effect prediction, will add annotations to INFO filed in VCF file under a tag named as "ANN". The annotations contains several fields separated by "|". eg.:

1. Allele

2. Annotation

3. Annotation_Impact

4. Gene_Name

5. Gene_ID

6. Feature_Type

7. Feature_ID

8. Transcript_BioType

9. Rank

10. HGVS.c

11. HGVS.p

12. cDNA.pos/cDNA.length ... ...

However, the INFO in hapResults may missing annotations that we need. In this case, we can custom INFOs in hapSummarys with addINFO(). Once the needed annotations were included in hap results, we can display them with plotHapTable() by specify the value of INFO_tag.

Value

ggplot2 object

See Also

addINFO()

Examples

data("geneHapR_test")
plotHapTable(hapResult)

geneHapR documentation built on May 29, 2024, 11:59 a.m.