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 = require('biojs-vis-scatter-plot');

var options = {
   background_colour: "white",
   background_stroke_colour:  "black",
   background_stroke_width:  "1px",
   circle_radius: {small: 2, large: 3.5},//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", , 8.93]],
   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: [0,100],
   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 = new app(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.