Package: helixpc
A series of scripts for gene database automation. Developed for the
Philippe Campeau Laboratory.InstallationhelixPC is available onPyPI, and is easily installable
throughpip.For stability, it is recommended that you install this package in avirtual environment, but
you may skip this step if you do not know how to set these up.$ pip install helixpcThat’s it! You may now call the script with:$ helixpcUsageGenerating 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
commandgroupcan help you generate one automatically. Simply stick
all your batches in a single csv file, call the utility and a file
namedoutput.csvwill 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 each values by passing an integer to[--round]or[-r]. The integer passed is equivalent to the number of decimal
places. For example, passing-r=2will round all values to the
nearest hundredth.You may pass the name of the output file with[--output]. If not
used, the output file name will default tooutput.csvinput file format:Check the examplegroup_input.csvThe first row should specify the column titles.Youmustcall the columns containing gene namesgene_symbol,
they are used as columns of reference by the scripts.Using the graphing utility$ helixpc graph <graph_input> [--heat] [--scatter] [--alpha] [--pvalues] <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:-s|--scatterSpecifies 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.-he|--heatSpecifies that you want a heat graph. It will graph both control and
samples. It accepts--no-logto prevent taking log_2() of all
values. All other passed functions are ignored (for now).<control>Specifies the control. You may give the 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 sample. You may give the 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. You may specify many samples, simply put
a space in between each.-a|--alphaSpecifies the alpha value. If used, you must also specify a column
that will serve as the colour value for each gene. See--pvalues.-p|--pvaluesOnce you have specified an alpha, you must specify column(s) whose
value for each gene will be compared to the alpha value. Everything
below (including) the alpha value will be colored red. Everything strictly above
the alpha will be colored black.e.g. :helixpc graph output.csv-s-p=X9760.raw-a=50002,3 4-l|--labelSpecifies the column to be used for making labels. The ten lowest and
ten highest values will be labelled on the graph.e.g. :helixpc graph output.csv-s-l=X9760.rawX9753 X9763-nl|--no-legendBy default, a legend is provided on the right hand side. Since this is
not very useful for standard, unicolour graphs, you may turn this off
by passing –no-legend.-nlg|--no-logBy default, the x and y coordinates will use the log_2 of the values
given. This tends to give clearer graphs, as it reduces their tendency
to elongate in a very thin shape, whilst still representing an
accurate distribution. You can turn this off by simply passing
–no-log.-nd|--no-diagonalBy default, a diagonal x=x line will be drawn on the graph. You may
turn this off by passing –no-diagonal.input file format:Check the examplegraph_input.csvThe first row should specify
the column titles.The first col should containgene_symbol