Mercurial > repos > fubar > plotly_tabular_tool
view plotly_tabular_tool/plotlytabular.xml @ 2:08cc7a481af8 draft
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author | fubar |
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date | Fri, 28 Jul 2023 06:01:53 +0000 |
parents | 449c918bc4cd |
children | 51a0c2e0fbdf |
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<tool name="plotlytabular" id="plotlytabular" version="3.0"> <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay--> <!--Created by toolfactory@galaxy.org at 28/07/2023 15:52:28 using the Galaxy Tool Factory.--> <description>Plotly plot generator for any small-ish Galaxy tabular data.</description> <requirements> <requirement version="1.5.3" type="package">pandas</requirement> <requirement version="5.9.0" type="package">plotly</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal"/> </stdio> <version_command><![CDATA[echo "3.0"]]></version_command> <command><![CDATA[python $runme --input_tab $input_tab --htmlout $htmlout --xcol "$xcol" --ycol "$ycol" --colourcol "$colourcol" --hovercol "$hovercol" --title "$title" --header "$header"]]></command> <configfiles> <configfile name="runme"><![CDATA[#raw import argparse import sys import math import plotly.express as px import pandas as pd # Ross Lazarus July 2023 # based on various plotly tutorials parser = argparse.ArgumentParser() a = parser.add_argument a('--input_tab',default='') a('--header',default='') a('--htmlout',default="test_run.html") a('--xcol',default='') a('--ycol',default='') a('--colourcol',default='') a('--hovercol',default='') a('--title',default='Default plot title') args = parser.parse_args() isColour = False isHover = False if len(args.colourcol.strip()) > 0: isColour = True if len(args.hovercol.strip()) > 0: isHover = True df = pd.read_csv(args.input_tab, sep='\t') MAXLEN=35 NCOLS = df.columns.size defaultcols = ['col%d' % (x+1) for x in range(NCOLS)] testcols = df.columns if len(args.header.strip()) > 0: newcols = args.header.split(',') if len(newcols) == NCOLS: df.columns = newcols else: sys.stderr.write('#### Supplied header %s has %d comma delimited header names - does not match the input tabular file %d columns - using col1,...coln' % (args.header, len(newcols), NCOLS)) df.columns = defaultcols else: # no header supplied - check for a real one that matches the x and y axis column names colsok = (args.xcol in testcols) and (args.ycol in testcols) # if they match, probably ok...should use more code and logic.. if not colsok: sys.stderr.write('replacing first row of data derived header %s with %s' % (testcols, defaultcols)) df.columns = defaultcols #df['col11'] = [-math.log(x) for x in df['col11']] # convert so large values reflect statistical surprise if isHover and isColour: fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol) elif isHover: fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol) elif isColour: fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol) else: fig = px.scatter(df, x=args.xcol, y=args.ycol) if args.title: ftitle=dict(text=args.title, font=dict(size=50)) fig.update_layout(title=ftitle) for scatter in fig.data: scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']] scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']] if len(args.colourcol.strip()) == 0: sl = str(scatter['legendgroup']) if len(sl) > MAXLEN: scatter['legendgroup'] = sl[:MAXLEN] fig.write_html(args.htmlout) #end raw]]></configfile> </configfiles> <inputs> <param name="input_tab" type="data" optional="false" label="Tabular input file to plot" help="" format="tabular" multiple="false"/> <param name="xcol" type="text" value="sepal_length" label="x axis for plot" help="Use a column name from the header if the file has one, or use one from the list supplied below, or use col1....colN otherwise to select the correct column"/> <param name="ycol" type="text" value="sepal_width" label="y axis for plot" help="Use a column name from the header if the file has one, or use one from the list supplied below, or use col1....colN otherwise to select the correct column"/> <param name="colourcol" type="text" value="petal_width" label="column containing a groupable variable for colour. Default none." help="Adds a legend so choose wisely "/> <param name="hovercol" type="text" value="species_id" label="columname for hover string" help="Use a column name from the header if the file has one, or use one from the list supplied below, or use col1....colN otherwise to select the correct column"/> <param name="title" type="text" value="Iris data" label="Title for the plot" help="Special characters will probably be escaped so do not use them"/> <param name="header" type="text" value="" label="Use this comma delimited list of column header names for this tabular file. Default is None when col1...coln will be used" help="Default for Galaxy blast outputs with 25 columns. The column names supplied for xcol, ycol, hover and colour MUST match either the supplied list, or if none, col1...coln."/> </inputs> <outputs> <data name="htmlout" format="html" label="htmlout" hidden="false"/> </outputs> <tests> <test> <output name="htmlout" value="htmlout_sample" compare="sim_size" delta="5000"/> <param name="input_tab" value="input_tab_sample"/> <param name="xcol" value="sepal_length"/> <param name="ycol" value="sepal_width"/> <param name="colourcol" value="petal_width"/> <param name="hovercol" value="species_id"/> <param name="title" value="Iris data"/> <param name="header" value=""/> </test> </tests> <help><![CDATA[ This is a generic version of the plotlyblast specific blastn Galaxy search output file plotter. .. class:: warningmark NOTE: Long strings in x and y tickmarks WILL BE TRUNCATED if they are too long - ".." is added to indicate truncation - otherwise some plots are squished. .. class:: warningmark NOTE: Columns with very small scientific notation floats will need to be pre-scaled in a way that doesn't confuse plotly.express with their values. ---- The main reason to run this tool is to have an interactive hover text specified so it appears when hovering over each data point to supply useful information. Assumes you want a hover display for an interactive plot to be informative Column names are auto-generated as col1,...coln unless a comma separated list of column names is supplied as the header parameter. For example, using a Galaxy blastn output with 25 columns, the following comma delimited string supplied as the "header" parameter will match the names of each column. qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles When a header is supplied, the xcol and other column names must match one of those supplied column names. So for example, xcol = "qaccver" for the blastn header example rather than xcol = "col1" when no header is supplied. Relies on Plotly python code released under the MIT licence: https://github.com/plotly/plotly.py/blob/master/LICENSE.txt ------ Script:: import argparse import sys import math import plotly.express as px import pandas as pd # Ross Lazarus July 2023 # based on various plotly tutorials parser = argparse.ArgumentParser() a = parser.add_argument a('--input_tab',default='') a('--header',default='') a('--htmlout',default="test_run.html") a('--xcol',default='') a('--ycol',default='') a('--colourcol',default='') a('--hovercol',default='') a('--title',default='Default plot title') args = parser.parse_args() isColour = False isHover = False if len(args.colourcol.strip()) > 0: isColour = True if len(args.hovercol.strip()) > 0: isHover = True df = pd.read_csv(args.input_tab, sep='\t') MAXLEN=35 NCOLS = df.columns.size defaultcols = ['col%d' % (x+1) for x in range(NCOLS)] testcols = df.columns if len(args.header.strip()) > 0: newcols = args.header.split(',') if len(newcols) == NCOLS: df.columns = newcols else: sys.stderr.write('#### Supplied header %s has %d comma delimited header names - does not match the input tabular file %d columns - using col1,...coln' % (args.header, len(newcols), NCOLS)) df.columns = defaultcols else: # no header supplied - check for a real one that matches the x and y axis column names colsok = (args.xcol in testcols) and (args.ycol in testcols) # if they match, probably ok...should use more code and logic.. if not colsok: sys.stderr.write('replacing first row of data derived header %s with %s' % (testcols, defaultcols)) df.columns = defaultcols #df['col11'] = [-math.log(x) for x in df['col11']] # convert so large values reflect statistical surprise if isHover and isColour: fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol) elif isHover: fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol) elif isColour: fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol) else: fig = px.scatter(df, x=args.xcol, y=args.ycol) if args.title: ftitle=dict(text=args.title, font=dict(size=50)) fig.update_layout(title=ftitle) for scatter in fig.data: scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']] scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']] if len(args.colourcol.strip()) == 0: sl = str(scatter['legendgroup']) if len(sl) > MAXLEN: scatter['legendgroup'] = sl[:MAXLEN] fig.write_html(args.htmlout) ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/bts573</citation> </citations> </tool>