biojs-vis-scatter-plot
BioJS component to provide a scatter-plot graphing tool hosted in Stemformatics
Getting Started
Install the module with: npm install biojs-vis-scatter-plot
for more details of the options, see the working example here and the example code here
var app = ; var options = background_colour: "white" background_stroke_colour: "black" background_stroke_width: "1px" circle_radius: small: 2 large: 35//3.5, // for the scatter points colour: colours data: data domain_colours : "#FFFFFF""#7f3f98" error_bar_width:5 error_dividor:100//100 means error bars will not show when error < 1% value //the graph size can be set to small (to fit multiple grpahs to a page) graph_size: "" height: small: 400 large: 1500 //horizontal lines takes a name, colour and the yvalue. If no colour is given one is chosen at random horizontal_lines: "Detection Threshold" "green" 5 "Median" 893 horizontal_line_value_column: 'value' //to have horizontal grid lines = width (to span accross the grid), otherwise = 0 horizontal_grid_lines: 0//width, legend_class: "legend" increment: number_of_increments legend_range: 0100 line_stroke_width: "2px" margin_legend: width - 10//width - 190, margin: top: 180 left:200 bottom: 530 right: 300 margin_small:top: 40 left: 40 bottom: 40 right: 80//default number of colours is 39 (before it ` reitterates over it again) number_of_colours: 39 probe_count: probe_count probes: probes //sample type order indicates whether or not the samplese need to be represented in a specific order //if no order is given then the order from the data set is taken sample_type_order:"none"// "DermalFibroblast, hONS", show_horizontal_line_labels: true subtitle1: subtitle1 subtitle2: subtitle2 stroke_width:"1.5px" target: target text_size: small: "12px" large: "20px" title: title title_class: "title" title_text_size: small: "12px" large: "30px" tip: tip//second tip to just display the sample type tooltip: tooltip // using d3-tips unique_id: "chip_id" watermark:"http://www1.stemformatics.org/img/logo.gif" width: small: 500 large: width // suggest 50 per sample x_axis_text_angle:-45 x_axis_title: "Samples" x_column: 'Sample_ID' x_middle_title: small: 200 large: 500 y_axis_title: "Log2 Expression" y_column: 'Expression_Value' var instance = options;
Documentation
Running the instance for developing
Note: If you are running Ubuntu LTS 12.04 or 14.04 you will be behind in npm. To fix this, do the following: Installing npm and node
sudo apt-get install npm
sudo apt-get update
May need to update the versions of npm and node
curl -o- https://raw.githubusercontent.com/creationix/nvm/v0.31.0/install.sh | bash
nvm install 5.0
Check you have an updated version of npm and node:
npm -v
(should be 3.3.6)
Install npm packages
npm install -g mkdirp
npm install -g browserify
npm install -g prunner
npm install -g sniper
Clone the repo of choice
git clone https://github.com/ArianeMora/bio-js-scatter-plot.git
Run
npm run build
npm run w
Once you have downloaded the code, you will need to ensure that you create a build directory in the root directory.
You can simply run the following command in the directory to see a website appear on localhost:9090
npm run w
Contributing
All contributions are welcome.
Support
If you have any problem or suggestion please open an issue here.
License
This software is licensed under the Apache 2 license, quoted below.
Copyright (c) 2015, ArianeMora
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.