BioJS component to provide a scatter plot graph hosted in Stemformatics
npm install biojs-vis-scatter-plot
> BioJS component to provide a scatter-plot graphing tool hosted in Stemformatics
npm install biojs-vis-scatter-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:
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
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.