biojs-vis-rohart-msc-test

BioJS component to provide a graph of the Rohart MSC Test hosted in Stemformatics

Getting Started

Install the module with: npm install biojs-vis-rohart-msc-test

for more details of the options, see the working example here and the example code here

var app = require('biojs-vis-rohart-msc-test');
 
var options = {
    background_colour: "white",
    background_stroke_colour:  "black",
    background_stroke_width:  "1px",
    circle_radius:5,  // for the scatter points
    data: data,
    data_columns_for_colour: ["MSC_calls","total_subsamplings"], //d.MSC_calls
    domain_colours : ["#FFFFFF","#7f3f98"],
    error_bar_width:10, 
    height: 1020,
    horizontal_line_value_column: 'value',
    horizontal_lines: horizontal_lines,  // this gets turned into an array of objects
    legend_class: "legend",
    legend_range: [0,100],
    margin:{top: 180, right: 120, bottom: 530, left: 200},
    sample_type_order: "BM MSC,BM erythropoietic cells CD235A+,BM granulopoietic cells CD11B+,BM hematopoietic cells CD45+,Developing cortex neural progenitor cells,Ventral midbrain neural progenitor cells,Olfactory lamina propria derived stem cells",
    show_horizontal_line_labels: true,
    subtitle1: subtitle1,
    subtitle2: subtitle2,
    target: target,
    title: title,
    title_class: "title",
    tooltip: tooltip, // using d3-tips
    unique_id: "chip_id",
    watermark:"http://www1.stemformatics.org/img/logo.gif",
    width:width, // suggest 50 per sample
    x_axis_text_angle:-45, 
    x_axis_title: "Samples",
    x_column:'Replicate_Group_ID',
    x_middle_title: 325,
    y_axis_title: "Rohart Score",
    y_column:'prediction' // d.prediction
}
 
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:

sudo apt-get purge nodejs npm
 
curl -sL https://deb.nodesource.com/setup | sudo bash -
 
sudo apt-get install -y nodejs
 
sudo npm install -g watchify biojs-sniper
 

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, rowlandm

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.