Open CEPHAS-01 opened 9 months ago
Thank you for the feedback. Could you mind sending your data and the running script to me at ylilin@163.com? I will check it out for the issue.
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.
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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
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
Thanks a bunch. So, the window size has to be at least 1e6?
actually not, it's just a general setting.
Alright, thanks.
On Thursday, October 12, 2023 at 09:18:51 PM PDT, Lilin Yin ***@***.***> wrote:
actually not, it's just a general setting.
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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.