EnrichedHeatmap
make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.
Science Score: 36.0%
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Repository
make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.
Basic Info
- Host: GitHub
- Owner: jokergoo
- License: other
- Language: R
- Default Branch: master
- Homepage: http://jokergoo.github.io/EnrichedHeatmap/
- Size: 44.4 MB
Statistics
- Stars: 194
- Watchers: 12
- Forks: 26
- Open Issues: 23
- Releases: 0
Metadata Files
README.md
Make Enriched Heatmaps
Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. It is broadly used to visualize e.g. how histone marks are enriched to specific sites.
There are several tools that can make such heatmap (e.g. ngs.plot or deepTools). Here we implement Enriched heatmap by ComplexHeatmap package. Since this type of heatmap is just a normal heatmap but with some fixed settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating a list of heatmaps to show correspondance between differnet data sources.
Citation
Zuguang Gu, et al., EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations, 2018. BMC Genomics. link
Install
EnrichedHeatmap is available on Bioconductor, you can install it by:
{r}
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("EnrichedHeatmap")
If you want the latest version, install it directly from GitHub:
{r}
library(devtools)
install_github("jokergoo/ComplexHeatmap")
install_github("jokergoo/EnrichedHeatmap")
Example
Like other tools, the task involves two steps:
- Normalize the accosiations between genomic signals and target regions to a matrix.
- Draw heatmaps.
{r}
mat1 = normalizeToMatrix(H3K4me3, tss, value_column = "coverage",
extend = 5000, mean_mode = "w0", w = 50)
mat2 = normalizeToMatrix(meth, tss, value_column = "meth", mean_mode = "absolute",
extend = 5000, w = 50, background = NA, smooth = TRUE)
{r}
partition = kmeans(mat1, centers = 3)$cluster
lgd = Legend(at = c("cluster1", "cluster2", "cluster3"), title = "Clusters",
type = "lines", legend_gp = gpar(col = 2:4))
ht_list = Heatmap(partition, col = structure(2:4, names = as.character(1:3)), name = "partition",
show_row_names = FALSE, width = unit(3, "mm")) +
EnrichedHeatmap(mat1, col = c("white", "red"), name = "H3K4me3", row_split = partition,
top_annotation = HeatmapAnnotation(lines = anno_enriched(gp = gpar(col = 2:4))),
column_title = "H3K4me3") +
EnrichedHeatmap(mat2, name = "methylation",
top_annotation = HeatmapAnnotation(lines = anno_enriched(gp = gpar(col = 2:4))),
column_title = "Methylation") +
Heatmap(log2(rpkm+1), col = c("white", "orange"), name = "log2(rpkm+1)",
show_row_names = FALSE, width = unit(5, "mm"))
draw(ht_list, main_heatmap = "H3K4me3", gap = unit(c(2, 10, 2), "mm"))
Also when signals are discreate values. E.g. chromatin states:
Actually you can generate rather complex heatmaps:
License
MIT @ Zuguang Gu
Owner
- Name: Zuguang Gu
- Login: jokergoo
- Kind: user
- Location: Heidelberg, Germany
- Company: German Cancer Research Center
- Website: http://jokergoo.github.io
- Repositories: 28
- Profile: https://github.com/jokergoo
A bioinformagician
GitHub Events
Total
- Issues event: 3
- Watch event: 5
- Issue comment event: 1
- Fork event: 1
Last Year
- Issues event: 3
- Watch event: 5
- Issue comment event: 1
- Fork event: 1
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Zuguang Gu | j****o@g****m | 213 |
| Zuguang Gu | z****u@d****e | 25 |
| Nitesh Turaga | n****a@g****m | 14 |
| Dan Tenenbaum | d****a@f****g | 6 |
| J Wokaty | j****y@s****u | 6 |
| Herve Pages | h****s@f****g | 4 |
| Hervé Pagès | h****s@f****g | 3 |
| vobencha | v****n@r****g | 3 |
| vobencha | v****a@g****m | 2 |
| d.tenenbaum | d****m@b****8 | 2 |
| z.gu | z****u@b****8 | 2 |
| LiNk-NY | m****9@g****m | 1 |
| Peter Hickey | p****y@g****m | 1 |
| mtmorgan@fhcrc.org | m****n@f****g@b****8 | 1 |
| Martin Morgan | m****n@f****g | 1 |
| James Hester | j****r@f****g | 1 |
| j.hester | j****r@b****8 | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 87
- Total pull requests: 3
- Average time to close issues: 3 months
- Average time to close pull requests: about 12 hours
- Total issue authors: 48
- Total pull request authors: 3
- Average comments per issue: 2.79
- Average comments per pull request: 0.33
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jokergoo (15)
- crazyhottommy (11)
- dktanwar (5)
- olechnwin (5)
- lakhanp1 (3)
- amechakra (2)
- AlicePsyche (2)
- francisfa (2)
- sameet (2)
- yamihn (2)
- ATpoint (1)
- lifengJGI (1)
- MorillonLab (1)
- dougbarrows (1)
- danphillips28 (1)
Pull Request Authors
- stkmrc (1)
- PeteHaitch (1)
- sameet (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 64,691 total
- Total dependent packages: 5
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: EnrichedHeatmap
Making Enriched Heatmaps
- Homepage: https://github.com/jokergoo/EnrichedHeatmap
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/EnrichedHeatmap/inst/doc/EnrichedHeatmap.pdf
- License: MIT + file LICENSE
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Latest release: 1.38.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- ComplexHeatmap >= 2.11.0 depends
- GenomicRanges * depends
- R >= 3.6.0 depends
- grid * depends
- methods * depends
- GetoptLong * imports
- IRanges * imports
- Rcpp * imports
- circlize >= 0.4.5 imports
- locfit * imports
- matrixStats * imports
- stats * imports
- utils * imports
- RColorBrewer * suggests
- genefilter * suggests
- knitr * suggests
- markdown * suggests
- rmarkdown * suggests
- testthat >= 0.3 suggests