The maximum number of markers in windows is smaller than the lower boundary of breaks

[CEPHAS-01]

Hi,
Thanks for this great tool.
I made use of it to visualize just 1 chromosome and it worked right.

I am trying to visualize 2 chromosomes but I get an error message.
"Error in Pmap[, 1] : incorrect number of dimensions"

When I tried again with only one of the 2 chromosomes I get the following

Error in DensityPlot(Pmap[, 1], Pmap[, 2], chr.ori, chr.pos.max = chr.pos.max, :
the maximum number of markers in windows is smaller than the lower boundary of breaks.

Here is a part (boundary) of the input for the 2 chromosomes plot:

RBMX Y 59362343
RBMX Y 59386279
PSMB6 Y 59458668
PLCXD1 Y-RefSeq 34576
LOC100298830 Y-RefSeq 54425
LOC132342097 Y-RefSeq 67594
LOC132344459 Y-RefSeq 287024

Thanks in advance for your help.

[YinLiLin]

Thank you for the feedback.
Could you mind sending your data and the running script to me at [email protected]? I will check it out for the issue.

[CEPHAS-01]

Hi,Thanks so much for your feedback.I will get the information together and send across to you. Warm regards, Temitayo On Saturday, October 7, 2023 at 01:19:53 AM PDT, Lilin Yin ***@***.***> wrote: Thank you for the feedback. Could you mind sending your data and the running script to me at ***@***.***? I will check it out for the issue. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[CEPHAS-01]

Hello, Here is the code and the file is attached. library("CMplot") dataCM <- read.table(file="CMPlot2.txt",header=T,sep="\t") CMplot(dataCM,plot.type="d",bin.size=1e1,chr.den.col=c("darkgreen", "yellow", "red"),file="jpg",file.name="CMPlotOutput",dpi=300, main="genes",file.output=TRUE,verbose=TRUE,width=9,height=3) Thanks so much for your help. Temitayo On Monday, October 9, 2023 at 04:26:46 PM PDT, Olagunju Temitayo ***@***.***> wrote: Hi,Thanks so much for your feedback.I will get the information together and send across to you. Warm regards, Temitayo On Saturday, October 7, 2023 at 01:19:53 AM PDT, Lilin Yin ***@***.***> wrote: Thank you for the feedback. Could you mind sending your data and the running script to me at ***@***.***? I will check it out for the issue. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***> gene chr pos UBE2D4 Y 26482682 ZNF280BY Y 26582882 UBE2D1 Y 26797405 ZNF280A Y 27159671 ZNF280A Y 27358396 HSFY1 Y 27484158 UBE2D3 Y 27665523 HSFY1 Y 27783314 UBE2D2 Y 28015252 ZNF280BY Y 28197926 ZNF280BY Y 28864480 ZNF280BY Y 29344345 HSFY1 Y 29675819 HSFY1 Y 29846305 UBE2D3 Y 30224209 ZNF280BY Y 30323456 env&ca Y 30527250 UBE2D3 Y 30818589 ZNF280A&sh Y 30889719 Zfp280b Y 31110801 UBE2D3 Y 31211081 HSFY1 Y 31218309 Gm19457 Y 31534073 UBE2D3 Y 31615896 ZNF280A Y 31884832 UBE2D3 Y 32277714 UBE2D1 Y 32996128 HSFY2 Y 33038989 UBE2D4 Y 33047554 HSFY2 Y 33090333 HSFY2 Y 33183575 LOC112443502 Y 33247978 UBE2D4 Y 33546774 UBE2D3 Y 33624133 ZNF280B Y 33910251 LOC112443502 Y 33920204 UBE2D1 Y 34072129 UBE2D1 Y 34458379 UBE2D4 Y 34781224 LOC112443502 Y 34877004 LOC104969408 Y 34880584 ZNF280BY Y 34888659 UBE2D1 Y 35110385 ZNF280A&sh Y 35181557 ZNF280B Y 35402916 Gm19457 Y 35503296 LOC104969408 Y 35917215 ZNF280BY Y 35925284 ZNF280BY Y 36166724 UBE2D3 Y 41773926 UBE2D1 Y 42159720 ENOSF1 Y 42168446 HSFY1 Y 42175491 HSFY2 Y 42405921 Gm19457 Y 42414464 ZNF280B Y 49271175 LOC104969408 Y 49279474 UBE2D2 Y 49704216 ZNF280B Y 50080053 ENOSF1 Y 50115807 ZNF280BY Y 50321044 LOC104969408 Y 50329325 ZNF280BY Y 50843291 ZNF280A&sh Y 51064373 UBE2D2 Y 51136844 ZNF280BY Y 51310583 LOC104969408 Y 51318869 HSFY2 Y 51426575 ENOSF1 Y 51731604 UBE2D1 Y 51739310 UBXN8 Y 52280349 ZNF280BY Y 52289066 ZNF280BY Y 52942379 LOC104969408 Y 52950693 LOC112443502 Y 52952345 HSFY2 Y 53111597 UBXN8 Y 53178913 LOC104969408 Y 53179542 HSFY2 Y 53616076 LOC132344573 Y-RefSeq 9192022 LOC132344574 Y-RefSeq 9199421 LOC132344575 Y-RefSeq 9228925 LOC132344576 Y-RefSeq 9236322 LOC132344577 Y-RefSeq 9243718 LOC132344578 Y-RefSeq 9251121 LOC132344579 Y-RefSeq 9265914 LOC132344580 Y-RefSeq 9273311 LOC132344581 Y-RefSeq 9325056 LOC132344582 Y-RefSeq 9332467 LOC132344583 Y-RefSeq 9339878 LOC132344584 Y-RefSeq 9347293 LOC132344585 Y-RefSeq 9354706 LOC132344586 Y-RefSeq 9362111 LOC132344587 Y-RefSeq 9435132 LOC132344588 Y-RefSeq 9442531 LOC132344589 Y-RefSeq 9449928 LOC132344590 Y-RefSeq 9457325 LOC132344627 Y-RefSeq 17451663 LOC132344628 Y-RefSeq 17514015 LOC132344483 Y-RefSeq 17535771 LOC132344437 Y-RefSeq 17550556 LOC132344484 Y-RefSeq 17901134 LOC132344629 Y-RefSeq 17963609 LOC132344630 Y-RefSeq 18231140 LOC132344485 Y-RefSeq 18291988 LOC132344486 Y-RefSeq 18318637 LOC132344632 Y-RefSeq 18380991 LOC132344487 Y-RefSeq 18399540 LOC132344488 Y-RefSeq 18415242 LOC132344489 Y-RefSeq 18430837 LOC132344490 Y-RefSeq 18834943 LOC132344491 Y-RefSeq 18938371 LOC132344492 Y-RefSeq 18954070 LOC132344493 Y-RefSeq 18969769 LOC132344494 Y-RefSeq 18985467 LOC132344495 Y-RefSeq 19001166 LOC132344496 Y-RefSeq 19016862 LOC132344497 Y-RefSeq 19032561 LOC132344498 Y-RefSeq 19352388 LOC132344635 Y-RefSeq 19414859 LOC132344636 Y-RefSeq 19796866 LOC132344499 Y-RefSeq 19857498 LOC132344500 Y-RefSeq 19884273 LOC132344638 Y-RefSeq 19946598 LOC132344501 Y-RefSeq 19967206 LOC132344639 Y-RefSeq 21033471 LOC132344502 Y-RefSeq 21094826 LOC132344503 Y-RefSeq 21648882 LOC132344641 Y-RefSeq 21669364 LOC132344504 Y-RefSeq 21730444 LOC132344505 Y-RefSeq 21758958 LOC132344643 Y-RefSeq 21821980 LOC132344644 Y-RefSeq 22029414 LOC528601 Y-RefSeq 22091185 LOC132344506 Y-RefSeq 22118032 LOC132344507 Y-RefSeq 22201128 LOC132344508 Y-RefSeq 22216844 LOC132344509 Y-RefSeq 22232545 LOC132344510 Y-RefSeq 22248246 LOC132344511 Y-RefSeq 22263819 LOC132344512 Y-RefSeq 22279535 LOC132344513 Y-RefSeq 22295235 LOC132344647 Y-RefSeq 22831062 LOC132344514 Y-RefSeq 22892353 LOC132344649 Y-RefSeq 23048127 LOC132342092 Y-RefSeq 23093760 LOC132344515 Y-RefSeq 23229408 LOC132344656 Y-RefSeq 24365794 LOC132344657 Y-RefSeq 24442280 LOC132344658 Y-RefSeq 24469013 LOC104974629 Y-RefSeq 24524743 LOC132344659 Y-RefSeq 24661639 LOC132344660 Y-RefSeq 24728184 LOC132344662 Y-RefSeq 25170370 LOC132344517 Y-RefSeq 25189455 LOC785023 Y-RefSeq 25210799 LOC132344518 Y-RefSeq 25232135 LOC132344519 Y-RefSeq 25253465 LOC132344520 Y-RefSeq 25274793 LOC112442075 Y-RefSeq 25296144 LOC132344521 Y-RefSeq 25317513 LOC132344522 Y-RefSeq 25338829 LOC132344538 Y-RefSeq 25345548 LOC789301 Y-RefSeq 25355837 LOC132344539 Y-RefSeq 25362551 LOC132344523 Y-RefSeq 25374188 LOC132344524 Y-RefSeq 25395401 LOC132344525 Y-RefSeq 25416725 LOC132344540 Y-RefSeq 25445725 LOC132344665 Y-RefSeq 25826189 LOC132344541 Y-RefSeq 25851473

[YinLiLin]

Hi @CEPHAS-01,

The version on GitHub has been updated for the issue you proposed, please source the online script and have a try. BTW, i found that you used a very small window size, it may not be an appropriate choice, i recommend using a bigger one, for example:

> source("https://raw.githubusercontent.com/YinLiLin/CMplot/master/R/CMplot.r")
> CMplot(dataCM,plot.type="d",bin.size=1e6,chr.den.col=c("darkgreen", "yellow", "red"),file="jpg",file.name="CMPlotOutput",dpi=300,main="genes",file.output=TRUE,verbose=TRUE,width=9,height=3,legend.cex=0.6)

Best,
LL

[CEPHAS-01]

Thanks a bunch.
So, the window size has to be at least 1e6?

[YinLiLin]

actually not, it's just a general setting.

[CEPHAS-01]

Alright, thanks. On Thursday, October 12, 2023 at 09:18:51 PM PDT, Lilin Yin ***@***.***> wrote: actually not, it's just a general setting. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>