BioJS component to provide a box plot graph or bar graph hosted in Stemformatics
npm install biojs-vis-violin-plot<<<<<<< HEAD
> BioJS component to provide a scatter-plot graphing tool hosted in Stemformatics
NOTE: CALCULATIONS ARE YET TO BE TESTED -> unit testing coming soon
npm install biojs-vis-box-plotfor more details of the options, see the working example here and the example code here
``javascript
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);
``
#### 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
All contributions are welcome.
If you have any problem or suggestion please open an issue here.
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.
=======