| Next changeset 1:e9268619b503 (2018-04-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plot_correlation_matrix commit 8451e17775c0ffcd7fa63ef65081f442bef91496 |
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added:
plot_corr.py plot_corr.xml test-data/1.txt test-data/2.txt test-data/3.txt test-data/corr.pdf test-data/corr.png test-data/corr.tab |
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| diff -r 000000000000 -r 0cee38fb62af plot_corr.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plot_corr.py Fri Apr 27 09:48:24 2018 -0400 |
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| @@ -0,0 +1,51 @@ +import os +import click +import matplotlib +matplotlib.use('tkagg') + +import pandas as pd # noqa: E402 +import seaborn as sns # noqa: E402 + + +def get_dataframe(files, labels, column, skiprows=1, sep='\t'): + d = {} + for file, label in zip(files, labels): + d[label] = pd.read_csv(file, usecols=[column], sep=sep, skiprows=skiprows, header=None, squeeze=True) + return pd.DataFrame.from_dict(d) + + +def plot_correlation(df, plot_path=None, method='pearson', correlation_matrix_path=None, figsize=(12, 12)): + corr = df.corr(method=method) + if correlation_matrix_path: + corr.to_csv(correlation_matrix_path, sep="\t") + if plot_path: + g = sns.clustermap(corr, annot=True, method="centroid", figsize=figsize, cbar_kws={'label': "%s correlation" % method}) + g.fig.suptitle("Cluster based on %s correlation for all samples" % method) + g.savefig(plot_path, bbox_inches='tight') + + +@click.command() +@click.argument("files", type=click.Path(exists=True), nargs=-1, required=True) +@click.option("-c", "--column", help="Use this numeric column to calculate correlation across files", default=1, required=True) +@click.option("--labels", help="File containing a list of labels, one label per line. Must match number of files", type=click.Path(exists=True), required=False) +@click.option("--plot_path", help="Write correlation plot to this path", type=click.Path(exists=False), required=False) +@click.option("--correlation_matrix_path", help="Write correlation plot to this path", type=click.Path(exists=False), required=False) +@click.option("--method", help="Use this method for calculating the correlation", required=False, type=click.Choice(['pearson', 'spearman', 'kendall'])) +@click.option("--skiprows", help="Skip this number of rows", required=False, default=0) +@click.option("--sep", help="Use this field separator when reading files", required=False, default="\t") +def main(files, column, labels=None, method="pearson", skiprows=1, plot_path=None, correlation_matrix_path=None, figsize=(12, 12), sep='\t'): + """Plot heatmap of pearson correlation and/or write matrix of pearson correlation values.""" + if labels: + labels = [l.strip() for l in open(labels) if l.strip()] + assert len(labels) == len(files), "Got %d files for plotting, but %d labels. Label and file length must be equal" % (len(files), len(labels)) + if not labels: + labels = [os.path.basename(f) for f in files] + if column != -1: + # Adjust for 0-based column selection + column -= 1 + df = get_dataframe(files, labels, column=column, skiprows=skiprows, sep=sep) + plot_correlation(df, plot_path=plot_path, correlation_matrix_path=correlation_matrix_path, figsize=figsize, method=method) + + +if __name__ == '__main__': + main() |
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| diff -r 000000000000 -r 0cee38fb62af plot_corr.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plot_corr.xml Fri Apr 27 09:48:24 2018 -0400 |
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| @@ -0,0 +1,79 @@ +<tool id="plot_correlation" name="Plot correlations" version="0.1.3"> + <description>for multiple samples</description> + <requirements> + <requirement type="package" version="0.8.1">seaborn</requirement> + <requirement type="package" version="6.7">click</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/plot_corr.py' +#echo "".join(["'%s' " % f for f in $input_files]) +-c $c +--labels '$labels' +#if $plot_type != "None" + --plot_path output.$plot_type +#end if +--correlation_matrix_path $tab_output +--method $method +--skiprows $skiprows +#if $input_files[0].ext == 'csv' +--sep "," +#end if +#if $plot_type != "None" + && mv output.$plot_type plot +#end if + ]]></command> +<configfiles> + <configfile name="labels">#for f in $input_files +$f.element_identifier +#end for</configfile> +</configfiles> + <inputs> + <param name="input_files" type="data" multiple="true" format="tabular,csv" label="Select the files for which to calculate the correlation"/> + <param argument="-c" type="data_column" data_ref="input_files" value="1" label="Select the numeric column to use"/> + <param argument="--skiprows" type="integer" min="0" value="0" label="Skip the first N rows" help="Make sure that all values are numeric"/> + <param argument="--plot_type" type="select" label="Select the type of plot to produce"> + <option value="pdf">PDF</option> + <option value="png">PNG</option> + <option value="None">Don't output plot</option> + </param> + <param argument="--method" type="select" label="Select the correlation method"> + <option value="pearson">Pearson Correlation</option> + <option value="spearman">Spearman Correlation</option> + <option value="kendall">Kendall-Tau Correlation</option> + </param> + </inputs> + <outputs> + <data name="plot_output" format="pdf" from_work_dir="plot" label="${tool.name} plot on ${on_string}"> + <filter>str(plot_type) != "None"</filter> + <change_format> + <when input="plot_type" value="png" format="png"/> + </change_format> + </data> + <data name="tab_output" format="tabular" label="${tool.name} table on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="input_files" value="1.txt,2.txt,3.txt" ftype="tabular"/> + <output name="plot_output" value="corr.pdf" ftype="pdf"/> + <output name="tab_output" value="corr.tab" ftype="tabular"/> + </test> + <test> + <param name="input_files" value="1.txt,2.txt,3.txt" ftype="tabular"/> + <param name="plot_type" value="png"/> + <output name="plot_output" value="corr.png" ftype="png"/> + <output name="tab_output" value="corr.tab" ftype="tabular"/> + </test> + </tests> + <help><![CDATA[ +What it does +------------ + +This tool calculates the correlation for a selected colum across many datasets. + +Example output: +--------------- + +.. image:: $PATH_TO_IMAGES/corr.png + + ]]></help> +</tool> |
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| diff -r 000000000000 -r 0cee38fb62af test-data/1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.txt Fri Apr 27 09:48:24 2018 -0400 |
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| diff -r 000000000000 -r 0cee38fb62af test-data/2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.txt Fri Apr 27 09:48:24 2018 -0400 |
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| diff -r 000000000000 -r 0cee38fb62af test-data/3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3.txt Fri Apr 27 09:48:24 2018 -0400 |
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| @@ -0,0 +1,199 @@ +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +-0.00516453559818209 +-0.0205481328793524 +-0.0307134820917063 +0.643067329643611 +1.55327354658444 +2.05395883600638 +1.8485408786659 +1.82516135186822 +1.6217760889074 +1.62897705755179 +0.971182460361824 +0.156660883535125 +0.127775374015235 +0.135010755726777 +0.542939010074629 +0.744330138490134 +0.597246050412643 +0.657133070688299 +0.346534408347958 +-0.0245163429088547 +-0.0139431460176159 +-0.0103487933749282 +-0.0103106492052688 +-0.0154384717774205 +-0.03829076379033 +-0.0607867125996615 +-0.0479737996899171 +0.0966985442338963 +0.0800373111167644 +-0.00773988693300774 +-0.00773988693300774 +0.390707120926344 +0.84557965619107 +0.68862282176212 +0.252380557759054 +0.578661190397868 +2.67747479840647 +3.06299611887981 +2.51938197834922 +1.9661531133494 +2.7005379234909 +3.57941962956699 +2.0372572607031 +1.74881150691715 +2.7673496630897 +2.64626125313048 +2.94407556915418 +0.519799593798434 +-0.12883780640624 +0.032334599017083 +0.569621956213534 +0.260212608552839 +0 +-0.0154384717774205 +-0.0307134820917063 +0.165837377212996 +0.908892576494339 +1.99701663216898 +1.56011053456701 +0.66338446079209 +0.0339859538062707 +-0.0151027085132735 +0.421833511505335 +0.118090946049965 +-0.0154384717774205 +-0.00399886774792812 +0.120535390215508 +-0.0119747604416604 +-0.118006428596147 +-0.102289217979718 +-0.109088998145182 +-0.411680278962258 +-0.35809957947193 +-0.253555441247913 +-0.135915307930659 +-0.287532814323564 +-0.728591834224069 +-1.11303503477544 +-0.619145980148498 +-0.259915666746712 +0.436406900825769 +0.349079400982403 +0.0405931055914946 +-0.242916799233507 +-0.0836047687464678 +0.0565601134633812 +0.0284212689385437 +-0.163380839539776 +-0.484596736082457 +-0.332896053948832 +-0.40354898270941 +-0.648090691311062 +-0.338823373781745 +-0.287758240179105 +0.500525235802173 +-0.0729205133690652 +-0.401658865500543 +0.629195126721701 +0.758631057489393 +1.09143642596256 +0.565345036665179 +0.163201739198077 +-0.0598547120512539 +-0.258379203064883 +0.123968606604721 +0.203131608539123 +0.20277939185342 +0.0313742103972228 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0.141086272493922 +0.707959960298169 +0.173000900218851 +-0.105128197823929 +-0.00773988693300774 +0.103510624785032 +-0.148181584376348 +-0.293877189116431 +-0.193187017449263 +0.129553618242327 +-0.00983965633013711 +0.0278223912802781 +-0.686754347603887 +-0.388633393547178 +-0.0326841598036203 +0.0182494822016573 +-0.349675044282807 +-0.202442038801667 +-0.167197985214767 +0.029749358080811 +0.272032074411685 +0.0205281145027709 +-0.0724479907461126 +0.0195170611639227 +0.155199750844578 +0.432032883161112 +0.432032883161112 +0.678959692548691 +0.861347033282818 +1.65249778123284 +2.42202818938149 +4.15845547013568 +3.54858169138378 +2.77629728427456 +2.01251615020891 +0.426321746003957 +0.143329923099115 +-0.0360137424037682 +-0.0278351723545067 +0.00479719455674217 +0.195861339146108 +0.213625337630196 +-0.117951109200658 +-0.117951109200658 |
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| diff -r 000000000000 -r 0cee38fb62af test-data/corr.pdf |
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| diff -r 000000000000 -r 0cee38fb62af test-data/corr.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/corr.tab Fri Apr 27 09:48:24 2018 -0400 |
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| @@ -0,0 +1,4 @@ + 1.txt 2.txt 3.txt +1.txt 1.0 0.9240450294117696 0.8726802298055488 +2.txt 0.9240450294117696 1.0 0.9784345740033148 +3.txt 0.8726802298055488 0.9784345740033148 1.0 |
