groupsはアルファベット順に自動でソートされ可視化されるが、他の規則で並べたい場合もある。
その場合、事前にユーザーが自身でソートしていることを想定し、新たにソートしないオプションがほしい。

また、ソートされると、ヒートマップ横のラベルの位置がずれたり、組成がおかしくなる。
groupsとgroup_colorsはソートされるが、groupsに所属される数などの計算はソートされる前のもので計算されているかも？

Defining track properties

tt <- c("sc", "add", "bed" "gene")
should be :
tt <- c("sc", "add", "bed" , "gene")?
adding one more comma in the end

Hi @yuifu,

The tool you developed seems very nice and I would like to use it for on my dataset.
Before starting I would like to check something with you and that I didn't understand from the documentation.

I have a BAM file for my scRNA that was generated from CellRanger or STAR solo. It contains all the reads with all barcodes. Shall I generate the bigwig file from this BAM file or shall I split it in 1 BAM file per cell?

I found another issue #3 where you mention that the user needs to split the BAM into single cell BAM using bxtools. But the previous issues does not seem to be solved.

Can you let me know how I should proceed?

Best wishes,

Jihed

Good day,

I would like to know whether I can use your tool to check coverage in 10x genomics data. My aim is to check the coverage in some specific chromosomes per cluster. I have tumor samples and, as many others do, I assign malignant cells to those that have CNV (based on transcriptomics data). I want to visualize and confirm that some clusters lack genes on those specific chromosomes (loss). Is it possible to use Millefy for this purpose? can I get a plot similar to the one used for the example, but instead of depicting two conditions, divide the gene coverage per cell cluster?

Thanks in advance!

If I change "heatmap" to "coverage", then it is giving error. Otherwise Heatmap is fine.

l <- millefyPlot(track_data=tdlist, track_type=tt, heights=heights,

•       sc_type = "coverage",
  

•       chr = chr, start = start, end = end,
  

•       sc_avg = TRUE, sc_avg_height = 4,
  

•       sc_sort_destiny = 'all',
  

•       title = text_main)
  

[1] "Begin millefyPlot: 2022-10-09 09:55:19"
[1] "title" "sc" "avg" "gene" "axis"
Error in plotScCoverageTrack(track_data[[i]], select, nbin, binsize, sc_avg) :
could not find function "plotScCoverageTrack"

Hi i have the following question. If we first use the option sc_sort_destiny = 'group' or sc_sort_destiny = 'all' for one plot for one chromosomal region. Is it possible to plot the same cells in the same order as they were plotted for that initial region in another plot for a different region? i.e. is the final order of traces in the plot being stored somewhere?