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1 <tool name="plotlytabular" id="plotlytabular" version="3.0">
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2 <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
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1
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3 <!--Created by toolfactory@galaxy.org at 28/07/2023 13:36:22 using the Galaxy Tool Factory.-->
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4 <description>Plotly plot generator</description>
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5 <requirements>
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6 <requirement version="1.5.3" type="package">pandas</requirement>
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7 <requirement version="5.9.0" type="package">plotly</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal"/>
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11 </stdio>
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12 <version_command><![CDATA[echo "3.0"]]></version_command>
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13 <command><![CDATA[python
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14 $runme
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15 --input_tab
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16 $input_tab
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17 --htmlout
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18 $htmlout
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19 --xcol
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20 "$xcol"
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21 --ycol
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22 "$ycol"
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23 --colourcol
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24 "$colourcol"
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25 --hovercol
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26 "$hovercol"
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27 --title
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28 "$title"
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29 --header
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30 "$header"]]></command>
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31 <configfiles>
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32 <configfile name="runme"><![CDATA[#raw
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33
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34 import argparse
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35 import sys
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36 import math
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37 import plotly.express as px
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38 import pandas as pd
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39 # Ross Lazarus July 2023
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40 # based on various plotly tutorials
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41 parser = argparse.ArgumentParser()
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42 a = parser.add_argument
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43 a('--input_tab',default='')
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44 a('--header',default='')
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45 a('--htmlout',default="test_run.html")
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46 a('--xcol',default='')
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47 a('--ycol',default='')
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48 a('--colourcol',default='')
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49 a('--hovercol',default='')
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50 a('--title',default='Default plot title')
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51 args = parser.parse_args()
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1
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52 isColour = False
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53 isHover = False
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54 if len(args.colourcol.strip()) > 0:
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55 isColour = True
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56 if len(args.hovercol.strip()) > 0:
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57 isHover = True
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58 df = pd.read_csv(args.input_tab, sep='\t')
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59 MAXLEN=35
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60 NCOLS = df.columns.size
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61 defaultcols = ['col%d' % (x+1) for x in range(NCOLS)]
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1
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62 testcols = df.columns
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63 if len(args.header.strip()) > 0:
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64 newcols = args.header.split(',')
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65 if len(newcols) == NCOLS:
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66 df.columns = newcols
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67 else:
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68 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))
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69 df.columns = defaultcols
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70 else: # no header supplied - check for a real one that matches the x and y axis column names
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71 colsok = (args.xcol in testcols) and (args.ycol in testcols) # if they match, probably ok...should use more code and logic..
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72 if not colsok:
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73 sys.stderr.write('replacing supplied header %s over existing %s' % (testcols, defaultcols))
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74 df.columns = defaultcols
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75 #df['col11'] = [-math.log(x) for x in df['col11']] # convert so large values reflect statistical surprise
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76 if isHover and isColour:
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77 fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol)
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78 elif isHover:
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79 fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol)
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80 elif isColour:
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81 fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol)
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82 else:
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83 fig = px.scatter(df, x=args.xcol, y=args.ycol)
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84 if args.title:
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85 ftitle=dict(text=args.title, font=dict(size=50))
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86 fig.update_layout(title=ftitle)
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87 for scatter in fig.data:
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88 scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']]
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89 scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']]
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90 if len(args.colourcol.strip()) == 0:
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91 sl = str(scatter['legendgroup'])
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92 if len(sl) > MAXLEN:
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93 scatter['legendgroup'] = sl[:MAXLEN]
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94 fig.write_html(args.htmlout)
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95
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96
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97 #end raw]]></configfile>
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98 </configfiles>
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99 <inputs>
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100 <param name="input_tab" type="data" optional="false" label="Tabular input file to plot" help="" format="tabular" multiple="false"/>
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101 <param name="xcol" type="text" value="sepal_length" label="x axis for plot" help=""/>
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102 <param name="ycol" type="text" value="sepal_width" label="y axis for plot" help=""/>
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103 <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 "/>
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104 <param name="hovercol" type="text" value="species_id" label="columname for hover string" help=""/>
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105 <param name="title" type="text" value="Iris data sepal length by sepal width coloured by petal width with species_id as the hover column" label="Title for the plot" help="Special characters will probably be escaped so do not use them"/>
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106 <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."/>
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107 </inputs>
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108 <outputs>
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109 <data name="htmlout" format="html" label="htmlout" hidden="false"/>
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110 </outputs>
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111 <tests>
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112 <test>
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113 <output name="htmlout" value="htmlout_sample" compare="sim_size" delta="5000"/>
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114 <param name="input_tab" value="input_tab_sample"/>
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1
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115 <param name="xcol" value="sepal_length"/>
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116 <param name="ycol" value="sepal_width"/>
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117 <param name="colourcol" value="petal_width"/>
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118 <param name="hovercol" value="species_id"/>
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119 <param name="title" value="Iris data sepal length by sepal width coloured by petal width with species_id as the hover column"/>
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0
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120 <param name="header" value=""/>
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121 </test>
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122 </tests>
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123 <help><![CDATA[
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124
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125 This is a specialised version of a generic tabular file plotter tool plotlytabular
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126
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127
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128
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129 .. class:: warningmark
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130
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131 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.
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132
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133
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134
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135 .. class:: warningmark
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136
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137 NOTE: Blast evalues WILL BE TRANSFORMED using -log10(evalue), so they are scaled in a way that doesn't confuse plotly.express with the tiny values.
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138
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139
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140
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141 ----
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142
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143
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144
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145 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.
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146
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147
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148
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149 Assumes you want a hover display for an interactive plot to be informative
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150
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151
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152
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153 Column names are auto-generated as col1,...coln unless a comma separated list of column names is supplied as the header parameter.
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154
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155
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156
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157 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.
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158
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159 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
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160
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161
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162
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163 When a header is supplied, the xcol and other column names must match one of those supplied column names.
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164
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165 So for example, xcol = "qaccver" for the blastn header example rather than xcol = "col1" when no header is supplied.
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166
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167
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168
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169 Relies on Plotly python code released under the MIT licence: https://github.com/plotly/plotly.py/blob/master/LICENSE.txt
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170
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171
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172
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173 .. image:: pbsample.png
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174
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175 :height: 400
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176
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177 :width: 400
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178
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179
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180
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181 ------
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182
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183
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184 Script::
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185
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186 import argparse
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187 import sys
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188 import math
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189 import plotly.express as px
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190 import pandas as pd
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191 # Ross Lazarus July 2023
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192 # based on various plotly tutorials
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193 parser = argparse.ArgumentParser()
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194 a = parser.add_argument
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195 a('--input_tab',default='')
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196 a('--header',default='')
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197 a('--htmlout',default="test_run.html")
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198 a('--xcol',default='')
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199 a('--ycol',default='')
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200 a('--colourcol',default='')
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201 a('--hovercol',default='')
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202 a('--title',default='Default plot title')
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203 args = parser.parse_args()
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1
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204 isColour = False
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205 isHover = False
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206 if len(args.colourcol.strip()) > 0:
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207 isColour = True
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208 if len(args.hovercol.strip()) > 0:
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209 isHover = True
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0
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210 df = pd.read_csv(args.input_tab, sep='\t')
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211 MAXLEN=35
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212 NCOLS = df.columns.size
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213 defaultcols = ['col%d' % (x+1) for x in range(NCOLS)]
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1
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214 testcols = df.columns
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0
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215 if len(args.header.strip()) > 0:
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216 newcols = args.header.split(',')
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217 if len(newcols) == NCOLS:
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218 df.columns = newcols
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219 else:
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220 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))
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221 df.columns = defaultcols
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1
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222 else: # no header supplied - check for a real one that matches the x and y axis column names
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223 colsok = (args.xcol in testcols) and (args.ycol in testcols) # if they match, probably ok...should use more code and logic..
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224 if not colsok:
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225 sys.stderr.write('replacing supplied header %s over existing %s' % (testcols, defaultcols))
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226 df.columns = defaultcols
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227 #df['col11'] = [-math.log(x) for x in df['col11']] # convert so large values reflect statistical surprise
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228 if isHover and isColour:
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229 fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol)
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230 elif isHover:
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231 fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol)
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232 elif isColour:
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233 fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol)
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234 else:
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235 fig = px.scatter(df, x=args.xcol, y=args.ycol)
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236 if args.title:
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237 ftitle=dict(text=args.title, font=dict(size=50))
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238 fig.update_layout(title=ftitle)
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239 for scatter in fig.data:
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240 scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']]
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241 scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']]
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242 if len(args.colourcol.strip()) == 0:
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243 sl = str(scatter['legendgroup'])
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244 if len(sl) > MAXLEN:
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245 scatter['legendgroup'] = sl[:MAXLEN]
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246 fig.write_html(args.htmlout)
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247
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248 ]]></help>
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249 <citations>
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250 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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251 </citations>
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252 </tool>
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253
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