| Title: | Gene Model Plotting in R |
| Date: | 2017-02-20 |
| Version: | 1.1.0 |
| Description: | Using simple input, this package creates plots of gene models. Users can create plots of alternatively spliced gene variants and the positions of mutations and other gene features. |
| Depends: | R (≥ 3.2.5) |
| Imports: | stringr |
| License: | GPL-2 |
| LazyData: | true |
| RoxygenNote: | 5.0.1 |
| URL: | https://github.com/greymonroe/genemodel |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2017-02-20 17:05:28 UTC; greymonroe |
| Author: | J Grey Monroe [aut, cre] |
| Maintainer: | J Grey Monroe <greymonroe@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2017-02-20 19:09:06 |
Gene model for AT5G62640
Description
Gene model for AT5G62640
Usage
AT5G62640
Format
A data frame with 32 rows and 2 variables:
- type
feature of gene ie intron exon or UTR
- coordinates
start and stop of gene feature separated by a "-"
...
Source
https://www.arabidopsis.org/servlets/TairObject?type=gene&id=1000654517
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", "coordinates" |
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.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")