Ecosyste.ms: Issues

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GitHub / bernatgel/karyoploter issues and pull requests

#152 - makeGenesDataFromTxDb did not pick up gene in some region

Issue - State: open - Opened by h20gg702 about 2 months ago - 2 comments
Labels: bug

#151 - documentation of kpAxis

Issue - State: open - Opened by Mitmischer 2 months ago

#150 - Calculate gene densities seperately from plotting

Issue - State: open - Opened by Mitmischer 2 months ago

#148 - kpHeatmap Fails when only one y value that is not 1

Issue - State: open - Opened by drneavin 5 months ago

#147 - kpAddCytobandLabels with custom genome and cytoband file fails

Issue - State: open - Opened by pkerbs 5 months ago - 3 comments

#146 - Individual Colors for Histone Tracks

Issue - State: closed - Opened by g-zavagno 6 months ago - 5 comments
Labels: usage question

#145 - Overlapping labels and huge gap between them

Issue - State: open - Opened by scienception 10 months ago - 1 comment

#144 - CNV heatmap clustering and metadata

Issue - State: open - Opened by auroramaurizio 11 months ago - 1 comment
Labels: enhancement

#143 - installation fail

Issue - State: closed - Opened by DittmanC about 1 year ago - 1 comment
Labels: usage question

#142 - Borders of chromosomes in plot type 6 are not all the same

Issue - State: closed - Opened by jsokol94 about 1 year ago - 1 comment

#141 - Error in graphics::par

Issue - State: closed - Opened by renee9904 about 1 year ago - 3 comments
Labels: usage question

#140 - highlighting telomeres (adding custom symbols to chromosome ends)

Issue - State: open - Opened by JWDebler about 1 year ago - 3 comments
Labels: enhancement

#139 - plotting bedgraph data for all chromosome at once

Issue - State: open - Opened by nirvana693 about 1 year ago - 6 comments
Labels: usage question

#138 - kpPlotGenes: Overlapping gene names margin increase

Issue - State: open - Opened by Hanuphant over 1 year ago - 3 comments

#137 - How would I use kpLines with kpPlotGenes?

Issue - State: closed - Opened by Hanuphant over 1 year ago - 1 comment

#136 - Change y-axis values

Issue - State: open - Opened by pailloufat-stack over 1 year ago
Labels: usage question

#135 - How to use karyoploteR for non-model species?

Issue - State: closed - Opened by Song-10-YF over 1 year ago - 1 comment
Labels: usage question

#134 - Blue bands on ideogram

Issue - State: closed - Opened by mkyriak over 1 year ago - 1 comment
Labels: usage question

#133 - plots bams that have no "chr"

Issue - State: closed - Opened by anuravi1234 over 1 year ago - 2 comments
Labels: usage question

#132 - some blocks are lacking in kpRect function

Issue - State: closed - Opened by zhoudreames over 1 year ago - 2 comments
Labels: usage question

#131 - kpBars will not change colors!

Issue - State: closed - Opened by shalvichirmade over 1 year ago - 2 comments
Labels: usage question

#130 - How to get plot name?

Issue - State: closed - Opened by DC-Jade over 1 year ago - 2 comments

#129 - How to get labels to not overlap other chromosomes?

Issue - State: open - Opened by yonniejon over 1 year ago - 2 comments
Labels: usage question

#127 - kpPlotManhattan not plotting manhattan plot

Issue - State: closed - Opened by Maetchild almost 2 years ago - 2 comments
Labels: usage question

#126 - auto adjust the Y-axis height

Issue - State: closed - Opened by nirvana693 about 2 years ago - 1 comment
Labels: usage question

#125 - kpHeatmap control colors

Issue - State: open - Opened by diyasen2021 about 2 years ago

#124 - Vary arch.height in kpPlotLinks

Issue - State: open - Opened by raunakms about 2 years ago - 1 comment
Labels: enhancement

#123 - kpPlotBigWig: added ability to start with a pre-loaded bigwig

Issue - State: closed - Opened by tovahmarkowitz about 2 years ago - 2 comments

#122 - Add legend to kpHeatmap plot

Issue - State: closed - Opened by diyasen2021 about 2 years ago - 2 comments

#121 - limit the coverage bar height

Issue - State: open - Opened by Rohit-Satyam about 2 years ago - 4 comments
Labels: enhancement, almostthere

#120 - Overlapping of Gene symbol in kpPlotGenes

Issue - State: open - Opened by JHKIM78 about 2 years ago

#119 - Bam coverage differences between chromosomes

Issue - State: open - Opened by diyasen2021 about 2 years ago - 2 comments
Labels: usage question

#118 - karyoploteR installation issue, macos 12

Issue - State: closed - Opened by AMJseattle over 2 years ago - 1 comment
Labels: question

#117 - Ploting gene density on my custom chromosomes

Issue - State: open - Opened by cell-c over 2 years ago - 1 comment
Labels: usage question

#116 - Chromosome positioning issues (2)

Issue - State: open - Opened by dansapozhnikov over 2 years ago - 3 comments
Labels: bug, usage question

#115 - Display of cytobands labels with plot.type =3

Issue - State: open - Opened by Vincgass over 2 years ago
Labels: bug

#114 - Incorrect Coordinates Chr. Labels

Issue - State: closed - Opened by merondun over 2 years ago - 4 comments
Labels: bug

#113 - plot.params margin - inconsistent settings

Issue - State: closed - Opened by jromanowska over 2 years ago - 1 comment
Labels: question

#112 - kpAddLabels does not draw labels on the right side

Issue - State: closed - Opened by jromanowska over 2 years ago - 2 comments
Labels: bug

#111 - How to add x axis title

Issue - State: closed - Opened by xiucz over 2 years ago - 2 comments
Labels: usage question

#110 - Rotated or staggered chromosome label, las argument?

Issue - State: closed - Opened by zx8754 over 2 years ago - 2 comments
Labels: enhancement

#109 - re: box plots

Issue - State: closed - Opened by mike-molnar almost 3 years ago - 1 comment
Labels: enhancement

#108 - about draw the plot

Issue - State: closed - Opened by zhoudreames almost 3 years ago - 1 comment
Labels: question

#107 - Customize labels on specific chromosome

Issue - State: closed - Opened by Zhuxitong almost 3 years ago - 2 comments
Labels: enhancement

#106 - BSgenomeForge new rat genome

Issue - State: open - Opened by motutaj about 3 years ago - 1 comment
Labels: question

#105 - Rainfall plot - value of y axis

Issue - State: open - Opened by sainadfensi about 3 years ago

#104 - flip the curve into opposite direction in the kpPlotLinks function?

Issue - State: closed - Opened by yxian9 about 3 years ago - 2 comments
Labels: bug, enhancement

#103 - kpPlotGenes colour by strand?

Issue - State: closed - Opened by yxian9 about 3 years ago - 2 comments

#102 - kpPlotMarkers getBM filters error

Issue - State: open - Opened by mehaffeym over 3 years ago

#101 - Error in loading custom genome

Issue - State: closed - Opened by jeff-godwin over 3 years ago - 5 comments
Labels: bug

#100 - problems with saving plot

Issue - State: closed - Opened by gabriellayi over 3 years ago - 3 comments
Labels: usage question

#99 - Trouble in color centromere

Issue - State: closed - Opened by KhanhLPBao over 3 years ago - 1 comment
Labels: usage question

#98 - seqlevelsStyle in plotKaryotype

Issue - State: open - Opened by bernatgel over 3 years ago
Labels: enhancement

#97 - notched centromeres

Issue - State: open - Opened by AGordonRobertson over 3 years ago
Labels: enhancement

#96 - remove cytobands

Issue - State: closed - Opened by gbdias over 3 years ago - 4 comments
Labels: enhancement, usage question

#95 - Issues with plotting using zoom fuction on server

Issue - State: closed - Opened by Mailinnia over 3 years ago - 8 comments
Labels: usage question

#94 - Handling BAM files with large chromosomes

Issue - State: open - Opened by Mailinnia over 3 years ago - 7 comments
Labels: question

#93 - saving several zoom in regions

Issue - State: open - Opened by mea2712 over 3 years ago - 5 comments
Labels: usage question

#92 - kpPlotRegions with bed file error?

Issue - State: open - Opened by TrentPrall over 3 years ago - 4 comments

#91 - clipping and r's

Issue - State: open - Opened by bernatgel over 3 years ago - 2 comments
Labels: bug

#90 - clipping on non-zoomed plots

Issue - State: open - Opened by bernatgel over 3 years ago - 2 comments
Labels: enhancement

#89 - add support for vertical karyograms

Issue - State: open - Opened by vdejager over 3 years ago - 1 comment
Labels: enhancement

#88 - add labels to top x% markers in a manhattan plot?

Issue - State: open - Opened by vdejager over 3 years ago - 1 comment
Labels: enhancement

#87 - multiple highlight colors in manhattanplot?

Issue - State: open - Opened by vdejager over 3 years ago - 1 comment
Labels: enhancement

#86 - kpPlotManhattan draws straight line when pvalues contains a zero

Issue - State: open - Opened by vdejager over 3 years ago
Labels: enhancement

#84 - manhattan plot 'chr' label crowding

Issue - State: open - Opened by wconnell almost 4 years ago

#83 - Error message trying to plot the Gallus gallus karyotype

Issue - State: open - Opened by ines3281 almost 4 years ago - 1 comment

#82 - Invalid seqlevels in kpPlotCoverage when a chromosome has no coverage

Issue - State: open - Opened by chaomacau almost 4 years ago - 4 comments
Labels: bug

#81 - normalize by the number of regions using kpPlotCoverage

Issue - State: open - Opened by shokohirosue almost 4 years ago
Labels: enhancement

#80 - Custom placement of chromosomes

Issue - State: closed - Opened by mrvollger almost 4 years ago - 2 comments

#79 - canfam3 genome

Issue - State: open - Opened by tderrien about 4 years ago

#78 - KaryoploteR for copy number

Issue - State: closed - Opened by rthapa1 about 4 years ago - 1 comment
Labels: usage question

#77 - customize size of chromosome labels on x-axis?

Issue - State: closed - Opened by conte1 about 4 years ago - 4 comments
Labels: usage question

#76 - Error plotKaryotype custom BSgenome

Issue - State: closed - Opened by Aworwui about 4 years ago - 1 comment

#75 - error on karyoploteR

Issue - State: closed - Opened by rthapa1 about 4 years ago - 2 comments
Labels: usage question

#74 - genome-wide visualization of copy number variation with karyoploteR

Issue - State: open - Opened by rthapa1 about 4 years ago - 5 comments
Labels: usage question

#73 - argument "times" invalid when trying to plot genes

Issue - State: closed - Opened by lbeltrame about 4 years ago - 3 comments
Labels: bug

#72 - New version and SNP-array data not working anymore

Issue - State: closed - Opened by carlacanedoribeiro about 4 years ago - 2 comments

#71 - Read chromosome lengths from fa/fai

Issue - State: open - Opened by bernatgel over 4 years ago
Labels: enhancement

#70 - Could not find function "addGeneNames" and "mergeTranscripts"

Issue - State: closed - Opened by Diwadkar over 4 years ago - 2 comments
Labels: wrong version, usage question

#69 - small region in kpPlotHorizon not rendering properly...

Issue - State: closed - Opened by njbowen over 4 years ago - 1 comment

#68 - Plotting a genome for GeneDensity

Issue - State: closed - Opened by Caro-Ca over 4 years ago - 5 comments
Labels: usage question

#67 - Loading Custom Genomes from GeneBank or similar

Issue - State: open - Opened by bernatgel over 4 years ago
Labels: enhancement

#66 - Add normalization.factor option to kpPlotBamCoverage and kpPlotBigWig

Issue - State: open - Opened by bernatgel over 4 years ago
Labels: enhancement

#65 - Latest master: cached cytobands corrupt?

Issue - State: closed - Opened by lbeltrame over 4 years ago - 10 comments

#64 - RFE: heatmap-like plot

Issue - State: closed - Opened by lbeltrame over 4 years ago - 5 comments
Labels: enhancement

#63 - Plot fail when genome has no cytobands

Issue - State: closed - Opened by bernatgel over 4 years ago - 1 comment
Labels: bug

#62 - coverage looks different than IGV

Issue - State: open - Opened by slowkow over 4 years ago - 3 comments
Labels: enhancement

#61 - kpPlotDensity extends over chromosome

Issue - State: closed - Opened by MatthewPearsonRA over 4 years ago - 3 comments
Labels: bug

#60 - Adding Base Numbers with plot.type = 6 (ideograms only)

Issue - State: open - Opened by etnite over 4 years ago - 3 comments
Labels: enhancement

#59 - The peaks of subgraphs have the same reduction.

Issue - State: closed - Opened by TheSallyGardens over 4 years ago - 1 comment

#58 - How to save plot into a png file?

Issue - State: closed - Opened by lakhujanivijay over 4 years ago - 2 comments
Labels: usage question

#57 - genome state HMM results for mm10

Issue - State: closed - Opened by TheSallyGardens over 4 years ago - 5 comments
Labels: usage question

#56 - kpPlotHorizon X chromosome bleeds off edge but only with negative values.....

Issue - State: closed - Opened by njbowen over 4 years ago - 6 comments
Labels: bug

#55 - How to adjust cytoband information to be present only at the location of copy number calls?

Issue - State: closed - Opened by lakhujanivijay over 4 years ago - 5 comments
Labels: usage question

#51 - Capture Karyoplots as a grob to allow combining with other grid graphics objects in composite plots

Issue - State: open - Opened by RichardJActon almost 5 years ago - 11 comments
Labels: usage question