plotGenes not work?

[shenweima]

this is my code

bdata <-read.table("gene.bed",header=T)
head(bdata)
chrom            = "SM_V7_1"
chromstart       = 33135620
chromend         = 33143037
plotGenes(bdata, chrom=chrom,chromstart = chromstart,chromend = chromend, types=bdata$type, maxrows=50,bheight=0.08,plotgenetype="box",bentline=FALSE,col="brown", labeloffset=.2,fontsize=0.9,arrowlength = 0.025,labeltext=TRUE)
labelgenome( chrom, chromstart,chromend,side=1,scipen=20,n=3,scale="Mb",line=.18,chromline=.5,scaleline=0.5)

Run this code in jutyter notebook. Only labelgenome() function work

chrom | start | stop | gene | score | strand | type
-- | -- | -- | -- | -- | -- | --
SM_V7_1 | 33135620 | 33135696 | Smp_012860.1 | . | 1 | CDS
SM_V7_1 | 33135730 | 33135847 | Smp_012860.1 | . | 1 | CDS
SM_V7_1 | 33135886 | 33136029 | Smp_012860.1 | . | 1 | CDS
SM_V7_1 | 33136062 | 33136237 | Smp_012860.1 | . | 1 | CDS
SM_V7_1 | 33137617 | 33137839 | Smp_012860.1 | . | 1 | CDS
SM_V7_1 | 33139243 | 33139362 | Smp_012860.1 | . | 1 | CDS
SM_V7_1 | 33140579 | 33140630 | Smp_012860.1 | . | 1 | CDS
SM_V7_1 | 33141423 | 33141616 | Smp_012860.1 | . | 1 | CDS
SM_V7_1 | 33142706 | 33142927 | Smp_012860.1 | . | 1 | CDS
SM_V7_1 | 33134853 | 33135619 | Smp_012860.1 | . | 1 | utr
SM_V7_1 | 33142926 | 33143037 | Smp_012860.1 | . | 1 | utr
SM_V7_1 | 33134851 | 33135030 | Smp_012860.2 | . | 1 | CDS
SM_V7_1 | 33136062 | 33136237 | Smp_012860.2 | . | 1 | CDS
SM_V7_1 | 33137617 | 33137839 | Smp_012860.2 | . | 1 | CDS
SM_V7_1 | 33139243 | 33139362 | Smp_012860.2 | . | 1 | CDS
SM_V7_1 | 33140579 | 33140630 | Smp_012860.2 | . | 1 | CDS
SM_V7_1 | 33141423 | 33141616 | Smp_012860.2 | . | 1 | CDS
SM_V7_1 | 33142706 | 33142927 | Smp_012860.2 | . | 1 | CDS
SM_V7_1 | 33134803 | 33134850 | Smp_012860.2 | . | 1 | utr
SM_V7_1 | 33142926 | 33143037 | Smp_012860.2 | . | 1 | utr
SM_V7_1 | 33135620 | 33135696 | g789.t1 | . | 1 | CDS
SM_V7_1 | 33135730 | 33135847 | g789.t1 | . | 1 | CDS
SM_V7_1 | 33135886 | 33136029 | g789.t1 | . | 1 | CDS
SM_V7_1 | 33136062 | 33136237 | g789.t1 | . | 1 | CDS
SM_V7_1 | 33137617 | 33137839 | g789.t1 | . | 1 | CDS
SM_V7_1 | 33139243 | 33139362 | g789.t1 | . | 1 | CDS
SM_V7_1 | 33140579 | 33140630 | g789.t1 | . | 1 | CDS
SM_V7_1 | 33141423 | 33141616 | g789.t1 | . | 1 | CDS
SM_V7_1 | 33142706 | 33142927 | g789.t1 | . | 1 | CDS
SM_V7_1 | 33134853 | 33135619 | g789.t1 | . | 1 | utr
SM_V7_1 | 33142926 | 33143037 | g789.t1 | . | 1 | utr

[dstern]

I am getting the same error. Coincides with upgrading to R 4.0. Fails also with Sushi-provided bed file

load("/Users/sternd/Downloads/Sushi_genes.bed.rda")
Sushi_genes.bed
chrom start stop gene score strand
1 chr15 73017309 73017438 COX5A . -1
2 chr15 72999672 72999836 COX5A . -1
3 chr15 73003042 73003164 COX5A . -1
4 chr15 73006160 73006281 COX5A . -1
5 chr15 73008510 73008626 COX5A . -1
plotGenes(Sushi_genes.bed)
[[1]]
NULL

[[2]]
function (n)
{
x <- ramp(seq.int(0, 1, length.out = n))
if (ncol(x) == 4L)
rgb(x[, 1L], x[, 2L], x[, 3L], x[, 4L], maxColorValue = 255)
else rgb(x[, 1L], x[, 2L], x[, 3L], maxColorValue = 255)
}
<bytecode: 0x7fcfc4dac3a0>
<environment: 0x7fcf9bfe4400>