tpoorten / Dotplotly
Licence: mit
Generate an interactive dot plot from mummer or minimap alignments
Stars: ✭ 92
Projects that are alternatives of or similar to Dotplotly
Falcon
Free, open-source SQL client for Windows and Mac 🦅
Stars: ✭ 4,848 (+5169.57%)
Mutual labels: plotly
Ig Follow Count
📈 A simple Instagram analytics tool that continuously logs and graphs your follower count.
Stars: ✭ 35 (-61.96%)
Mutual labels: plotly
Plotly express
Plotly Express - Simple syntax for complex charts. Now integrated into plotly.py!
Stars: ✭ 633 (+588.04%)
Mutual labels: plotly
Angularcomponentplotly
Angular Component for Plotly, ASP.NET Core, Elasticsearch
Stars: ✭ 14 (-84.78%)
Mutual labels: plotly
Scala Plotly Client
Visualise your data from Scala using Plotly
Stars: ✭ 39 (-57.61%)
Mutual labels: plotly
Pragmaticai
[Book-2019] Pragmatic AI: An Introduction to Cloud-based Machine Learning
Stars: ✭ 79 (-14.13%)
Mutual labels: plotly
Awesome Dash
A curated list of awesome Dash (plotly) resources
Stars: ✭ 1,085 (+1079.35%)
Mutual labels: plotly
React Plotly.js
A plotly.js React component from Plotly 📈
Stars: ✭ 701 (+661.96%)
Mutual labels: plotly
Visualization Of Global Terrorism Database
📊 Visualization of GTD with py Plotly lib, including amazing graphs and animation 📼
Stars: ✭ 16 (-82.61%)
Mutual labels: plotly
Hexapod Robot Simulator
A hexapod robot simulator built from first principles
Stars: ✭ 577 (+527.17%)
Mutual labels: plotly
Algorithm Playground
An (old) and unstructured (messy tbh) collection of programming exercises.
Stars: ✭ 75 (-18.48%)
Mutual labels: plotly
Colorcet
A set of useful perceptually uniform colormaps for plotting scientific data
Stars: ✭ 438 (+376.09%)
Mutual labels: plotly
Bubbly
A python package for plotting animated and interactive bubble charts using Plotly
Stars: ✭ 37 (-59.78%)
Mutual labels: plotly
Plotly.py
The interactive graphing library for Python (includes Plotly Express) ✨
Stars: ✭ 10,701 (+11531.52%)
Mutual labels: plotly
Pandoc Plot
Render and include figures in Pandoc documents using your plotting toolkit of choice
Stars: ✭ 75 (-18.48%)
Mutual labels: plotly
dotPlotly
Create an interactive dot plot from mummer output OR PAF format
R script that makes a plotly interactive and/or static (png/pdf) dot plot.
Shiny app available for testing
here)
Example (moreFor mummer (nucmer -> show-coords) output:
show-coords -c example.delta > example.coords
./mummerCoordsDotPlotly.R -i example.coords -o out -s -t -m 500 -q 500000 -k 7 -l
For PAF format (e.g. minimap2):
./pafCoordsDotPlotly.R -i example.paf -o out -s -t -m 500 -q 500000 -k 7 -l
Updates (10/29/17)
- Added script for PAF format
- Fixes for Mummer format script: add -t param, add handling of one ref chrom
Dependencies
The script requires three R packages: install.packages(c("optparse", "ggplot2", "plotly"))
.
Script parameters
Use ./mummerCoordsDotPlotly.R -h
to see options.
-i INPUT, --input=INPUT
coords file from mummer program 'show.coords' [default NULL]
-o OUTPUT, --output=OUTPUT
output filename prefix [default out]
-v, --verbose
Print out all parameter settings [default]
-q MIN-QUERY-LENGTH, --min-query-length=MIN-QUERY-LENGTH
filter queries with total alignments less than cutoff X bp [default 4e+05]
-m MIN-ALIGNMENT-LENGTH, --min-alignment-length=MIN-ALIGNMENT-LENGTH
filter alignments less than cutoff X bp [default 10000]
-p PLOT-SIZE, --plot-size=PLOT-SIZE
plot size X by X inches [default 15]
-l, --show-horizontal-lines
turn on horizontal lines on plot for separating scaffolds [default FALSE]
-k NUMBER-REF-CHROMOSOMES, --number-ref-chromosomes=NUMBER-REF-CHROMOSOMES
number of sorted reference chromosomes to keep [default all chromosmes]
-s, --similarity
turn on color alignments by percent similarity [default FALSE]
-t, --identity-on-target
turn on calculation of % identity for on-target alignments only [default FALSE]
-x, --interactive-plot-off
turn off production of interactive plotly [default TRUE]
-r REFERENCE-IDS, --reference-ids=REFERENCE-IDS
comma-separated list of reference IDs to keep [default NULL]
-h, --help
Show this help message and exit
Note that the project description data, including the texts, logos, images, and/or trademarks,
for each open source project belongs to its rightful owner.
If you wish to add or remove any projects, please contact us at [email protected].