trackViewer

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Re-adjust figure size of lollipopPlot and avoid x-axis cut off

1

Hi, Thank you for this great visualization tool. I am new to trackViewer lollipopPlot and I am experimenting with making the plot. However, my plot looked very wide and have...

nalomran

Plot with more than eight colors

1

Hi, I am using the lolliplot() function to create SNP plots along Zscore values. The problem is I have 16 categories for the SNPs and even if I define my...

rimjhimroy

hg 38 annotated variant file and TxDb.Hsapiens.UCSC.hg38.knownGene

4

Hi Jianhong I obtained my filtered .vcf which I annotated using hg38 using wannovar. However when I am using this to lolliplot using .vcf file using the "hg38" and "TxDb.Hsapiens.UCSC.hg38.knownGene"...

smeeta

lolliplot border width?

1

There is some method to change the width of lines that link the balloons without enlarge the text labels? Something like mut_GRange$border.stroke?

criphg

recommended parameter settings for lollipopPlot with large numbers of mutations

6

Hello, Thank you for such a useful package! I have generally found lollipopPlots produced using this package to look fantastic, however there are a number of genes where I want...

bkinnersley

getGeneIDsFromTxDb missing

3

Hi, Thank you for providing the great package, the getGeneIDsFromTxDb function is missing in the bioconductor version. Best

fengyq

Hi, I'm struggling to understand the calculations for positioning the y labels in tracks. It seems you are defining a viewport for the text grob in such a way that...

ripkrizbi

heightDist does not work

4

Hi, I faced a problem that heightDist does not work when I used the following script. Do you know the solution? Thank you. `A

h20gg702

Lolliplot plus with the coverage without geneTrack

8

Hi, Thank you for developing a beautiful package. I am trying to make the Lolliplot and bigwig the coverage data like below (paste screenshots). I know there are some examples...

h20gg702

addInteractionAnnotation function: Error in if (.dat2target[i]) { : missing value where TRUE/FALSE needed

1

I am unable to add lines dictating TAD boundaries onto my interaction data. The function "addInteractionAnnotation" found in the [(vignette)](https://www.bioconductor.org/packages/devel/bioc/vignettes/trackViewer/inst/doc/plotInteractionData.html) is not available in the trackViewer package, even with most...

audrwat