基因模型可视化R包说明说明书
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Package‘genemodel’
October13,2022
Title Gene Model Plotting in R
Date2017-02-20
Version1.1.0
Description
Using simple input,this package creates plots of gene ers can create plots of alterna-tively spliced gene variants and the positions of mutations and other gene features.
Depends R(>=3.2.5)
Imports stringr
License GPL-2
LazyData true
RoxygenNote5.0.1
URL https:///greymonroe/genemodel
Suggests knitr,rmarkdown
VignetteBuilder knitr
NeedsCompilation no
Author J Grey Monroe[aut,cre]
Maintainer J Grey Monroe<********************>
Repository CRAN
Date/Publication2017-02-2019:09:06
R topics documented:
AT5G62640 (2)
genemodel.plot (2)
mutation.plot (3)
Index4
1
2genemodel.plot AT5G62640Gene model for AT5G62640
Description
Gene model for AT5G62640
Usage
AT5G62640
Format
A data frame with32rows and2variables:
type feature of gene ie intron exon or UTR
coordinates start and stop of gene feature separated by a"-"...
Source
https:///servlets/TairObject?type=gene&id=1000654517
genemodel.plot genemodel.plot
Description
This function plots a gene model
Usage
genemodel.plot(model,start,bpstop,orientation,xaxis=TRUE)
Arguments
model data.frame containing model information.Required columns are"type","coor-dinates"
start start position
bpstop stop position
orientation either"foward"or"reverse"indicates the direction of transcription
xaxis default is TRUE and adds axis above gene model showing position Examples
data(AT5G62640)
genemodel.plot(AT5G62640,25149433,25152541,"reverse",xaxis=TRUE)
mutation.plot3 mutation.plot mutation.plot
Description
This function plots mutations along genemodels created with genemodel.plot
Usage
mutation.plot(start,stop,text="",drop=-0.15,col="red",
haplotypes=NULL)
Arguments
start start position
stop stop position
text any text that you want displayed on the label
drop how far below the gene model you want the mutation label to be placed
col the color of the text and mutation line to be
haplotypes the color of dots that you want to place along the mutation line to indicate some factor such as haplotype that the mutation belongs to
Examples
data(AT5G62640)
genemodel.plot(AT5G62640,25149433,25152541,"reverse")
mutation.plot(25149593,25149593,text="P->S",col="red",haplotype="blue")
Index
∗datasets
AT5G62640,2
AT5G62640,2
genemodel.plot,2
mutation.plot,3
4。