Ecosyste.ms: Issues

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GitHub / jokergoo/EnrichedHeatmap issues and pull requests

#87 - A heatmap with no signal

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

#86 - only use exons as target

Issue - State: open - Opened by jokergoo 6 months ago - 1 comment

#85 - enriched heatmap cut rows

Issue - State: open - Opened by yamihn 9 months ago

#84 - Modification of the position of color bar

Issue - State: open - Opened by ZixiaoWang17 9 months ago

#83 - Scale two heatmaps with EnrichedHeatmap

Issue - State: closed - Opened by noelletnw 10 months ago - 1 comment

#82 - Collapsing replicates

Issue - State: open - Opened by konsta-kukkonen about 1 year ago

#81 - same y-aixs for concatenated heatmap

Issue - State: open - Opened by gyanmishra about 1 year ago - 2 comments

#80 - Correct calculation of enrich score

Pull Request - State: open - Opened by stkmrc about 1 year ago

#78 - Strange subscript out of bounds error

Issue - State: open - Opened by yimingsun12138 over 1 year ago - 1 comment

#77 - strange plot Enrichedheatmap

Issue - State: open - Opened by yamihn over 1 year ago

#75 - Set order to row_split

Issue - State: closed - Opened by 14stutzmanav almost 2 years ago - 1 comment

#74 - remove failed_rows from matrix

Issue - State: open - Opened by Adnanhashim about 2 years ago - 1 comment

#73 - Empty matrix

Issue - State: open - Opened by michela12345 about 2 years ago - 1 comment

#72 - color for anno_enriched

Issue - State: open - Opened by olechnwin about 2 years ago - 2 comments

#71 - speed up normalizeToMatrix

Issue - State: open - Opened by olechnwin over 2 years ago - 2 comments

#70 - to-do-list

Issue - State: open - Opened by jokergoo over 2 years ago

#69 - How To? color top annotation lines by row_split variable?

Issue - State: closed - Opened by malcook over 2 years ago - 3 comments

#68 - Visualize multiple target regions in one graph

Issue - State: closed - Opened by xfchen0912 over 2 years ago - 2 comments

#67 - Filtering matrices by range name

Issue - State: closed - Opened by jantusan over 2 years ago - 5 comments

#66 - strand information

Issue - State: closed - Opened by MorillonLab over 2 years ago - 1 comment

#65 - maybe use mode "s" for the average line chart?

Issue - State: open - Opened by jokergoo almost 3 years ago

#64 - raster image too blur

Issue - State: open - Opened by jokergoo almost 3 years ago

#63 - border line of the target regions

Issue - State: open - Opened by jokergoo almost 3 years ago

#62 - plot multiple bigwig data in one heatmap?

Issue - State: open - Opened by junjunlab about 3 years ago - 2 comments

#61 - Smoothing methylation data causing very extreme values impacting visualization

Issue - State: closed - Opened by rauldiul about 3 years ago - 4 comments
Labels: enhancement

#60 - mean_mode error

Issue - State: closed - Opened by Jiang-cpu751 over 3 years ago - 5 comments

#59 - Can't get the picture

Issue - State: closed - Opened by chenchen-eng over 3 years ago - 4 comments

#58 - Image magick error for very large rasters

Issue - State: closed - Opened by RichardJActon over 3 years ago - 20 comments

#57 - Question about target_ratio in normalizeToMatrix

Issue - State: closed - Opened by AstreChen over 3 years ago - 2 comments

#56 - Trouble with scaling

Issue - State: closed - Opened by wilsoner2175 almost 4 years ago - 5 comments

#55 - Names of heatmap annotation

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

#54 - white line in raster

Issue - State: closed - Opened by ClarissaFeuersteinAkgoz about 4 years ago - 9 comments

#53 - Is there a way to only plot top curve?

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

#52 - how to use row_split and add annotation heatmap for the split

Issue - State: closed - Opened by olechnwin about 4 years ago - 3 comments

#51 - Setting number of breaks

Issue - State: closed - Opened by dktanwar over 4 years ago - 9 comments

#50 - annotation_legend_side does not work

Issue - State: closed - Opened by dktanwar over 4 years ago - 6 comments

#49 - Question: Setting `lwd` for all heatmaps

Issue - State: closed - Opened by dktanwar over 4 years ago - 2 comments

#48 - Height of column title box

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

#47 - Problem splitting by more than two groups in newest version (1.18.0)

Issue - State: closed - Opened by dougbarrows over 4 years ago - 2 comments

#46 - Strange V Shape when generating heatmap?

Issue - State: closed - Opened by Jome0169 almost 5 years ago - 3 comments

#45 - how can I manually cluster with EnrichedHeatMap?

Issue - State: closed - Opened by Yuxinagli almost 5 years ago - 1 comment

#44 - EnrichedHeatmap() Error: You should have at least two distinct break values.

Issue - State: closed - Opened by francisfa about 5 years ago - 3 comments

#43 - output bed regions along with each window coverage/score

Issue - State: closed - Opened by itsvenu about 5 years ago - 2 comments

#42 - About the "row_split" parameter？

Issue - State: closed - Opened by francisfa about 5 years ago - 2 comments

#40 - Custom ticks and label position at x-axis

Issue - State: closed - Opened by ATpoint over 5 years ago - 1 comment

#39 - Meaning of rows on heatmap

Issue - State: closed - Opened by AYYYang over 5 years ago - 1 comment

#38 - Mixed colors in top_annotations

Issue - State: closed - Opened by CharlesJB over 5 years ago - 10 comments

#37 - customer reference genes annotation

Issue - State: closed - Opened by skytguuu over 5 years ago - 4 comments

#36 - multiplemEnrichedheatmaps with only line plots

Issue - State: closed - Opened by Papareddy over 5 years ago - 1 comment

#35 - Colors of the top_annotation switch randomly

Issue - State: closed - Opened by jdekanter almost 6 years ago - 3 comments

#34 - Position line color not uniform for top annotation and main heatmap body

Issue - State: closed - Opened by lakhanp1 almost 6 years ago - 3 comments

#33 - Error while using show_error argument of anno_enriched()

Issue - State: closed - Opened by lakhanp1 almost 6 years ago - 2 comments

#31 - Suggestion: gpar() for heatmap border

Issue - State: closed - Opened by lakhanp1 about 6 years ago - 2 comments

#30 - flip a subset of the matrix before clustering rows

Issue - State: closed - Opened by crazyhottommy over 6 years ago - 5 comments

#29 - extend and w not working for categorical data

Issue - State: closed - Opened by crazyhottommy over 6 years ago - 4 comments

#28 - heatmap_legend_param does not work for discrete heatmaps

Issue - State: closed - Opened by jokergoo over 6 years ago

#27 - factor ordering for discrete values

Issue - State: closed - Opened by crazyhottommy over 6 years ago - 2 comments

#26 - Convert from continuous matrix to discrete matrix

Issue - State: closed - Opened by jokergoo over 6 years ago - 1 comment

#25 - clustering for chromatins state

Issue - State: closed - Opened by crazyhottommy over 6 years ago - 4 comments

#24 - support target with category values

Issue - State: closed - Opened by jokergoo over 6 years ago

#23 - Give an example for calculating correlation of binding and expression.

Issue - State: closed - Opened by sameet over 6 years ago - 1 comment

#22 - missing a line in the line graph on top of the heatmap

Issue - State: closed - Opened by lifengJGI over 6 years ago - 4 comments

#20 - row order when plotting multiple heatmap

Issue - State: closed - Opened by olechnwin about 7 years ago - 12 comments

#19 - add ticks on x-axis

Issue - State: closed - Opened by jokergoo about 7 years ago

#18 - 1 base pair shift when normalize to target regions

Issue - State: closed - Opened by jokergoo about 7 years ago - 3 comments

#17 - Adding rowname to enrichedHeatmap

Issue - State: closed - Opened by LucoLab over 7 years ago - 6 comments

#16 - Update normalize.R

Pull Request - State: open - Opened by sameet over 7 years ago

#15 - `getSignalsFromList` fails.

Issue - State: closed - Opened by sameet over 7 years ago - 5 comments

#14 - Typo

Pull Request - State: closed - Opened by PeteHaitch over 7 years ago - 1 comment

#13 - put `show_row_names` to the main argument

Issue - State: closed - Opened by jokergoo over 7 years ago

#12 - normalizeToMatrix, w for target

Issue - State: closed - Opened by jokergoo about 8 years ago

#11 - Target regions without extension

Issue - State: closed - Opened by sudhirthakurela over 8 years ago - 1 comment

#10 - Detail normalization method used by normalizeToMatrix ?

Issue - State: closed - Opened by AlicePsyche over 8 years ago - 4 comments

#9 - Use my own matrix instead of `normalizeToMatrix`

Issue - State: closed - Opened by AlicePsyche over 8 years ago - 11 comments

#7 - question on color scale on multiple heatmaps

Issue - State: closed - Opened by crazyhottommy over 8 years ago - 10 comments

#6 - normalizeToMatrix: do not want to extend, and target_ratio = 1

Issue - State: closed - Opened by crazyhottommy almost 9 years ago - 2 comments

#5 - impute DNA methylation when there is no CpG

Issue - State: closed - Opened by crazyhottommy almost 9 years ago - 2 comments

#4 - feature request: enrichment heatmap on genebody

Issue - State: closed - Opened by crazyhottommy almost 9 years ago - 2 comments

#3 - Error with normalizeToMatrix() when using "smooth = TRUE"

Issue - State: closed - Opened by ycl6 almost 9 years ago - 6 comments

#2 - SUGGESTION: More efficient code using matrixStats (>= 0.50.0)

Issue - State: closed - Opened by HenrikBengtsson almost 9 years ago - 1 comment

#1 - show an example to get H3K4me3 GRanges object

Issue - State: closed - Opened by crazyhottommy almost 9 years ago - 7 comments