Juan-Jose Garces

coOncoplot for GISTIC2 results

4

Hi (again) @PoisonAlien, And is there any trick to draw the coOncoplot for GISTIC2 results only? I've seen the #188 issue but I haven't a MAF file neither mutation information......

Axis wrongly adjusted

1

Hi @YinLiLin, I found your package very useful, thanks! In my case I'm plotting allele frequency not the p-value but I guess it's also possible... but I'm having an issue...

Error message using markerDiffTable() function: "invalid character indexing"

8

Hi @Xiaojieqiu I have the same problem that @ikwak2 (issue #20) but with the markerDiffTable function. It appears this error: `Error in intI(i, n = x@Dim[1], dn[[1]], give.dn = FALSE)...

`snp_index` must be size 0 or 1, not 2 [pileup_and_phase.R]

21

Hi, I'm running the first step (`pileup_and_phase.R`)... ``` Rscript pileup_and_phase.R \ --label x21922_mm8 \ --samples x21922_mm8 \ --bams /home/igoroz/jgarces/scCSCMM_sara/data/21922_mm8/outs/per_sample_outs/21922/count/sample_alignments.bam \ --barcodes /home/igoroz/jgarces/scCSCMM_sara/data/21922_mm8/outs/per_sample_outs/21922/count/sample_filtered_barcodes.csv \ --outdir x21922_mm8 \ --gmap Eagle_v2.4.1/tables/genetic_map_hg38_withX.txt.gz \ --snpvcf...

``` # future setting plan("multicore", workers = 20) # everything goes smoothly --> no more than 20 cores under usage aux2

Hi @jokergoo, thanks for so impressive tool, really amazing! I've read [this documentation](https://jokergoo.github.io/ComplexHeatmap/reference/anno_barplot.html) for creating a proportional barplot in my oncoprint but I'm a bit stuck about how to apply...

Hi. I'm having some problems with the recently added feature to split the visualization according to a second variable in the metadata. I tried it in `CoveragePlot` and `PlotFootprint`, and...

Meaning of numbers tree

1

Hi, I've read the [documentation](https://arxiv.org/pdf/1709.04412.pdf) and I'm not able to understand the meaning of numbers appearing in each tree leaf... In the example within the documentation (figure 2) appears that:...

Windows version of APT not compatible

2

Hi @CS-GustaveRoussy, Thanks for this marvelous pipeline. I'm having a problem I think with the Windows version I'm using... the error message (sorry because it's in spanish) says that this...

Add custom feature to plot

2

I'm doing some testing with _enclone_ for generating honey plots and it works nicely. I'd like to add a custom variable (eg, annotated cells for each barcode) and color according...