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Automisation of graph generation for gene FC databases.

Project description

A series of scripts for gene database automation. Developed for the Philippe Campeau Laboratory.

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Installation

helixPC is available on PyPI, and is easily installable through pip.

For stability, it is recommended that you install this package in a virtual environment, but you may skip this step if you do not know how to set these up.

$ pip install helixpc

That’s it! You may now call the script with:

$ helixpc

Usage

Generating a file for the graphing utility

$ helixpc group <group_input> [--nonan] [--round=[int]]

If you do not yet have a valid input file for graph generation, the command group can help you generate one automatically. Simply stick all your batches in a single csv file, call the utility and a file named output.csv will be generated. You can then feed to the graphing utility.

Please note that:

  • If certain genes are included multiple times, their mean will be calculated, and only a single entry will appear in the output.
  • You may pass [--nonan] or [-n] to omit any gene that are missing entries in a batch.
  • You may round by passing an integer to [--round] or [-r]. The integer passed is equivalent to the number of decimal places. For example, passing -r=2 will round all values to the nearest hundredth.

input file format:

  • Check the example group_input.csv
  • The first row should specify the column titles.
  • You must call the columns containing gene names gene_symbol, they are used as columns of reference by the scripts.

Using the graphing utility

$ helixpc graph <graph_input> [--heat] [--scatter] <control> <sample> [<sample> ...]

Once you have a csv file that you want to use for generating graph, you may feed it to the graphing utility. You must give the csv file a series of arguments for it to function properly:

--scatter

Specifies that you want scatter graph(s). Scatter graphs are generated with a control (always the same) in the x axis, and a sample in the y axis. Giving more than one sample will return to you multiple graphs, one for each sample. You can hover over each point to see the name of the gene it is representing.

--heat

Specifies that you want a heat graph. Not implemented yet.

<control>

Specifies the control. You may give an index or the name of a column. You may also give a series of indexes/column-names separated by a comma, and the values used will be the mean of each row for the series of columns given.

<sample>

Specifies the first sample. You may give an index or the name of a column. You may also give a series of indexes/column-names separated by a comma, and the values used will be the mean of each row for the series of columns given.

[<sample> ...]

indicates that you can give more than one sample, simply separate each sample with a space.

input file format:

  • Check the example graph_input.csv The first row should specify the column titles.
  • The first col should contain gene_symbol

Project details


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