A somewhat random list of nice data visualization type catalogs. Mostly taken from Yuri Engelhardt's tweet
Classic: https://datavizcatalogue.com
Thorough: http://datavizproject.com
Fritz Lekschas flekschas
👋
flekschas
/ rao-2014-gm12878-chr4-arrowhead-tads-hipiler-v140.csv
Last active
December 5, 2019 21:12
HiPiler CSV example: Arrowhead TAD calls for chromosome 4 from Rao et al. (2014) GM12878 including the corner score, U-var, L-var, U-sign, and L-sign. Go to http://hipiler.higlass.io and drag this file onto the page to explore the data.
We can make this file beautiful and searchable if this error is corrected: It looks like row 8 should actually have 17 columns, instead of 14. in line 7.
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| chrom1,start1,end1,strand1,chrom2,start2,end2,strand2,dataset,zoomOutLevel,server,coords,corner-score,U-var,L-var,U-sign,L-sign | |
| chr4,69285000,70075000,+,chr4,69285000,70075000,+,CQMd6V_cRw6iCI_-Unl3PQ,0,//higlass.io,hg19,0.098279,0.20712,0.43713,0.4001,0.40554 | |
| chr4,18680000,20260000,+,chr4,18680000,20260000,+,CQMd6V_cRw6iCI_-Unl3PQ,0,//higlass.io,hg19,0.58392,0.31563,0.32759,0.5282,0.42433 | |
| chr4,42985000,44635000,+,chr4,42985000,44635000,+,CQMd6V_cRw6iCI_-Unl3PQ,0,//higlass.io,hg19,0.71638,0.29186,0.32687,0.61341,0.53275 | |
| chr4,60060000,60985000,+,chr4,60060000,60985000,+,CQMd6V_cRw6iCI_-Unl3PQ,0,//higlass.io,hg19,0.60764,0.29093,0.28665,0.41713,0.40194 | |
| chr4,8640000,9145000,+,chr4,8640000,9145000,+,CQMd6V_cRw6iCI_-Unl3PQ,0,//higlass.io,hg19,0.80964,0.2152,0.33994,0.47216,0.60157 | |
| chr4,22960000,24440000,+,chr4,22960000,24440000,+,CQMd6V_cRw6iCI_-Unl3PQ,0,//higlass.io,hg19,0.6919,0.25365,0.22566,0.43577,0.53228 | |
| chr4,125265000,126205000,+,chr4,125265000,126205000,+,CQMd6V_cRw6iCI_-Unl3PQ,0,//higlass.io,hg19,0.96028, |
flekschas
/ data-visualization-type-catalogs.md
Created
May 14, 2018 14:09
Data Visualization Type Catalogs
flekschas
/ rao-2014-gm12878-template
Last active
June 17, 2018 22:50
This is a simplified template for a view configuration on Rao et al. (2014) GM12878 served from http://higlass.io. Please refer to https://github.com/flekschas/hipiler/wiki/Data#config-file how to configure the snippets (`fgm` part). In essence you need to replace the `fgm.fragments` with a double array of BEDPE like locations. This example cont…
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| { | |
| "fgm": { | |
| "fragmentsServer": "//higlass.io/api/v1/", | |
| "fragmentsPrecision": 2, | |
| "fragmentsDims": 60, | |
| "fragmentsPadding": 50, | |
| "fragmentsBaseRes": 1000, | |
| "fragmentsPercentile": 99, | |
| "fragmentsIgnoreDiags": 1, | |
| "fragments": [ |
flekschas
/ rao-2014-gm12878-mbol-1kb-mres-chr4-tads-hipiler-v140.json
Last active
December 5, 2019 21:17
HiPiler Example: TAD calls of Arrowhead for chromosome 4 from Rao et al. (2014) GM12878. TADs are normalized to 60x60 bins to support piling, the diagonal is excluded for better of-diagonal patterns, and the matrix is capped at the 99-percentile against outliers. See https://flekschas.github.io/hipiler/ for a live demo.
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| { | |
| "fgm": { | |
| "fragmentsServer": "//higlass.io/api/v1/", | |
| "fragmentsPrecision": 2, | |
| "fragmentsDims": 60, | |
| "fragmentsPadding": 50, | |
| "fragmentsBaseRes": 1000, | |
| "fragmentsPercentile": 99, | |
| "fragmentsIgnoreDiags": 1, | |
| "fragments": [ |
flekschas
/ rao-2014-gm12878-vs-k562-mbol-1kb-mres-telomeres-hipiler-v140.json
Last active
December 5, 2019 21:17
HiPiler Example: Telomere contacts from Rao et al. (2014) GM12878 vs K562. Using "group by location" and switching to the "variance cover mode" one can compare the telomeres in both cell lines. See https://flekschas.github.io/hipiler/ for a live demo.
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| { | |
| "fgm": { | |
| "fragmentsServer": "//higlass.io/api/v1/", | |
| "fragmentsPrecision": 2, | |
| "fragmentsNoBalance": true, | |
| "fragmentsDims": 60, | |
| "fragmentsBaseRes": 1000, | |
| "fragments": [ | |
| ["chrom1", "start1", "end1", "strand1", "chrom2", "start2", "end2", "strand2", "dataset", "zoomOutLevel", "cell-line"], | |
| ["chr1", 0, 1, "coding", "chr2", 0, 1, "coding", "CQMd6V_cRw6iCI_-Unl3PQ", 6, "GM12878"], |
flekschas
/ rao-2014-gm12878-mbol-1kb-mres-telomeres-hipiler-v140.json
Last active
December 5, 2019 21:15
HiPiler Example: Telomere contacts from Rao et al. (2014) GM12878. See https://flekschas.github.io/hipiler/ for a live demo.
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| { | |
| "fgm": { | |
| "fragmentsServer": "//higlass.io/api/v1/", | |
| "fragmentsPrecision": 2, | |
| "fragmentsNoBalance": true, | |
| "fragmentsDims": 60, | |
| "fragmentsBaseRes": 1000, | |
| "fragments": [ | |
| ["chrom1", "start1", "end1", "strand1", "chrom2", "start2", "end2", "strand2", "dataset", "zoomOutLevel"], | |
| ["chr1", 0, 1, "coding", "chr2", 0, 1, "coding", "CQMd6V_cRw6iCI_-Unl3PQ", 6], |
flekschas
/ rao-2014-gm12878-mbol-1kb-mres-chr22-loops-hipiler-v140.json
Last active
December 5, 2019 21:14
HiPiler Example: Loop calls for chromosome 22 from Rao et al. (2014) GM12878 including distance-to-diagonal, noise, and sharpness measures. See http://hipiler.higlass.io for a live demo.
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| { | |
| "fgm": { | |
| "fragmentsServer": "//higlass.io/api/v1/", | |
| "fragmentsPrecision": 2, | |
| "fragmentsDims": 22, | |
| "fragmentsBaseRes": 1000, | |
| "fragments": [ | |
| ["chrom1", "start1", "end1", "strand1", "chrom2", "start2", "end2", "strand2", "dataset", "zoomOutLevel", "size", "distance-to-diagonal", "noise", "sharpness", "_test"], | |
| ["chr22", 17395000, 17400000, "coding", "chr22", 17535000, 17540000, "coding", "CQMd6V_cRw6iCI_-Unl3PQ", 3, 25000000, 135000, 0.21559968240959723, 58.75532055518839, 1], | |
| ["chr22", 17400000, 17410000, "coding", "chr22", 17980000, 17990000, "coding", "CQMd6V_cRw6iCI_-Unl3PQ", 3, 100000000, 570000, 0.19905589933149648, 59.977490663167465, 1], |
flekschas
/ higlass-examples.json
Last active
February 1, 2017 00:20
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| [{ | |
| "url": "http://higlass.io/visualization/?config=B80L-PFiTLihXPGLcYvXbg", | |
| "title": "Viewport projection", | |
| "description": "Showing where the one view located by showing its position in another view", | |
| "image": "https://cloud.githubusercontent.com/assets/932103/22489607/698b0e46-e7e6-11e6-9ba2-41ef7e416cd8.png" | |
| }] |
flekschas
/ download_nsd.sh
Created
April 21, 2016 15:49
Grab all ISA-Tabs from Nature Scientific Data
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| #!/bin/bash | |
| # Download Nature Scientific Data ISA Tabs | |
| YEARS[0]=2014 | |
| YEARS[1]=2015 | |
| YEARS[2]=2016 | |
| NUM_ISA_TABS[0]=53 | |
| NUM_ISA_TABS[1]=76 |
Generates a random directed acyclic graph and serializes it in JSON
git clone https://gist.github.com/flekschas/0ea70dec4d92bc706e61 random-graph-json && cd random-graph-jsonmkvirtualenv -a $(pwd) random-graph-json[Optional but recommended]pip install -r requirements.txt