marker peaks track changed each time when using plotBrowserTrack

[jinbufan]

When I use plotBrowserTrack(), I found that the track plot pattern between marker peaks will change each time when I re-plotting with the same parameters, and the reason was y ranges changed each time, which showed as 'Coverage Norm. ATAC Signal Range (0−0.16) by ReadsInTSS'. Does anyone know how to change the ranges of y-axis? I tried to find the solution in the original code but I failed...
By the way, I tried to change 'ylim' parameter to 'c(0,0.9)' as previous discussion showed, but the actual plot's range turned to 0-0.03, I have no idea either.
I will really appreciate if someone could solve my problem. Please check the plot below for more details.

[rcorces]

You cannot specify a specific y axis limit, just a quantile limit. The tracks differ because of random sampling. Currently, the only way around this is implemented on the dev branch and you have to use the maxCells parameter and set it to a value larger than the maximum number of cells in any group. This effectively disables random sampling of cells.

[jinbufan]

Thanks for your reply! I try to set scCellsMax parameter in plotBrowserTrack() but the tracks are still differ, or should I set maxCells in addReproduciblePeakSet()? I'm sorry for this question but I really confused about it. Very thank you.

[ZennFangZhou]

did you deal with that question? i met same condition when i repeatly plot the tarcks, i found the result became opposite...

[jinbufan]

sorry but still not, maybe use signac for plotting will be better

[ZennFangZhou]

devtools::install_github("GreenleafLab/ArchR", ref="dev", repos = BiocManager::repositories(), force=TRUE). the code can install 1.0.3 version ArchR, you can plot tracks of all cells by para maxCells.