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1 <tool name="plotlyblast" id="plotlyblast" version="3.0">
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2 <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
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3 <!--Created by toolfactory@galaxy.org at 04/08/2023 10:36:02 using the Galaxy Tool Factory.-->
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4 <description>Plotly plot generator specialised for 25 column Galaxy blast search result tabular files</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 <requirement version="0.2.1" type="package">python-kaleido</requirement>
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1:" level="fatal"/>
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12 </stdio>
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13 <version_command><![CDATA[echo "3.0"]]></version_command>
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14 <command><![CDATA[python
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15 $runme
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16 --input_tab
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17 $input_tab
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18 --htmlout
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19 $htmlout
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20 --xcol
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21 "$xcol"
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22 --ycol
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23 "$ycol"
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24 --colourcol
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25 "$colourcol"
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26 --hovercol
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27 "$hovercol"
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28 --title
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29 "$title"
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30 --header
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31 "$header"
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32 --image_type
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33 "$outputimagetype"]]></command>
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34 <configfiles>
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35 <configfile name="runme"><![CDATA[#raw
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36
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37 import argparse
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38 import shutil
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39 import sys
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40 import math
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41 import plotly.express as px
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42 import pandas as pd
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43 # Ross Lazarus July 2023
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44 # based on various plotly tutorials
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45 # Expects a blastn search result passed in as the first command line parameter.
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46 parser = argparse.ArgumentParser()
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47 a = parser.add_argument
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48 a('--input_tab',default='')
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49 a('--header',default='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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50 a('--htmlout',default="test_run.html")
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51 a('--xcol',default='')
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52 a('--ycol',default='')
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53 a('--colourcol',default='')
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54 a('--hovercol',default='')
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55 a('--title',default='test blast plot')
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56 a('--image_type',default='short_html')
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57 args = parser.parse_args()
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58 df = pd.read_csv(args.input_tab, sep='\t')
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59 NCOLS = df.columns.size
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60 MAXLEN = 30 # tricky way to truncate long axis tickmarks
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61 defaultcols = ['col%d' % (x+1) for x in range(NCOLS)]
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62 if len(args.header.strip()) > 0:
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63 newcols = args.header.split(',')
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64 if len(newcols) == NCOLS:
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65 df.columns = newcols
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66 else:
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67 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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68 df.columns = defaultcols
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69 else:
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70 df.columns = defaultcols
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71 df['evalue'] = [-math.log(x + 1e-308) for x in df['evalue']] # convert so large values reflect statistical surprise
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72 if len(args.colourcol.strip()) == 0:
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73 fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol)
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74 else:
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75 fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol)
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76 if args.title:
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77 ftitle=dict(text=args.title, font=dict(size=40))
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78 fig.update_layout(title=ftitle)
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79 for scatter in fig.data:
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80 scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']]
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81 scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']]
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82 if len(args.colourcol.strip()) == 0:
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83 sl = str(scatter['legendgroup'])
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84 if len(sl) > MAXLEN:
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85 scatter['legendgroup'] = sl[:MAXLEN]
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86 if args.image_type == "short_html":
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87 fig.write_html(args.htmlout, full_html=False, include_plotlyjs='cdn')
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88 elif args.image_type == "long_html":
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89 fig.write_html(args.htmlout)
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90 elif args.image_type == "small_png":
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91 ht = 768
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92 wdth = 1024
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93 fig.write_image('plotly.png', height=ht, width=wdth)
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94 shutil.copyfile('plotly.png', args.htmlout)
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95 else:
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96 ht = 1200
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97 wdth = 1920
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98 fig.write_image('plotly.png', height=ht, width=wdth)
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99 shutil.copyfile('plotly.png', args.htmlout)
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100
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101
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102
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103 #end raw]]></configfile>
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104 </configfiles>
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105 <inputs>
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106 <param name="input_tab" type="data" optional="false" label="Tabular input file to plot" help="" format="tabular" multiple="false"/>
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107 <param name="xcol" type="text" value="qaccver" label="x axis for plot" help=""/>
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108 <param name="ycol" type="text" value="bitscore" label="y axis for plot" help=""/>
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109 <param name="colourcol" type="text" value="piden" label="column containing a groupable variable for colour. Default none." help="Adds a legend so choose wisely "/>
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110 <param name="hovercol" type="text" value="qseq" label="columname for hover string" help=""/>
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111 <param name="title" type="text" value="Qaccver by bitscore coloured by pident. Hover shows blast match." label="Title for the plot" help="Special characters will probably be escaped so do not use them"/>
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112 <param name="header" type="text" value="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" 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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113 <param name="outputimagetype" type="select" label="Select the output format for this plot image" help="Small and large png are not interactive but best for many (__gt__10k) points. Stand-alone HTML includes 3MB of javascript. Short form HTML gets it the usual way so can be cut and paste into documents.">
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114 <option value="short_html">Short HTML interactive - requires network connection to download 3MB javascript</option>
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115 <option value="long_html">Long HTML for stand-alone viewing where network access to libraries is not available.</option>
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116 <option value="large_png">Large (1920x1200) png image - not interactive so hover column ignored</option>
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117 <option value="small_png">Small (1024x768) png image - not interactive so hover column ignored</option>
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118 </param>
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119 </inputs>
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120 <outputs>
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121 <data name="htmlout" format="html" label="Plotlyblast $title on $input_tab.element_identifier" hidden="false">
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122 <change_format>
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123 <when input="outputimagetype" format="png" value="small_png"/>
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124 <when input="outputimagetype" format="png" value="large_png"/>
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125 </change_format>
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126 </data>
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127 </outputs>
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128 <tests>
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129 <test>
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130 <output name="htmlout" value="htmlout_sample" compare="sim_size" delta="5000"/>
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131 <param name="input_tab" value="input_tab_sample"/>
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132 <param name="xcol" value="qaccver"/>
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133 <param name="ycol" value="bitscore"/>
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134 <param name="colourcol" value="piden"/>
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135 <param name="hovercol" value="qseq"/>
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136 <param name="title" value="Qaccver by bitscore coloured by pident. Hover shows blast match."/>
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137 <param name="header" value="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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138 <param name="outputimagetype" value="short_html"/>
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139 </test>
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140 </tests>
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141 <help><![CDATA[
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142
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143 This is a specialised version of a generic tabular file plotter tool plotlytabular
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144
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145 PNG image outputs are not interactive but best for very large numbers of data points. Hover column will be ignored.
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146
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147 HTML interactive plots are best for a few thousand data points at most because
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148
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149 the hover information becomes uncontrollable with very dense points.
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150
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151 Using the shorter format HTML relies on internet access when viewed, and saves 3MB of javascript being embedded.
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152
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153 The long format is useful if potentially viewed offline.
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154
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155
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156
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157 .. class:: warningmark
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158
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159 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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160
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161
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162
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163 .. class:: warningmark
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164
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165 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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166
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167
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168
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169 ----
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170
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171
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172
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173 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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174
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175
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176
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177 Assumes you want a hover display for an interactive plot to be informative
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178
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179
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180
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181 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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182
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183
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184
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185 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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186
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187 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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188
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189
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190
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191 When a header is supplied, the xcol and other column names must match one of those supplied column names.
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192
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193 So for example, xcol = "qaccver" for the blastn header example rather than xcol = "col1" when no header is supplied.
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194
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195
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196
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197 Relies on Plotly python code released under the MIT licence: https://github.com/plotly/plotly.py/blob/master/LICENSE.txt
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198
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199
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200
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201
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202
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203
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204
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205 ------
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206
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207
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208 Script::
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209
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210 import argparse
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211 import shutil
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212 import sys
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213 import math
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214 import plotly.express as px
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215 import pandas as pd
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216 # Ross Lazarus July 2023
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217 # based on various plotly tutorials
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218 # Expects a blastn search result passed in as the first command line parameter.
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219 parser = argparse.ArgumentParser()
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220 a = parser.add_argument
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221 a('--input_tab',default='')
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222 a('--header',default='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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223 a('--htmlout',default="test_run.html")
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224 a('--xcol',default='')
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225 a('--ycol',default='')
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226 a('--colourcol',default='')
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227 a('--hovercol',default='')
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228 a('--title',default='test blast plot')
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229 a('--image_type',default='short_html')
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230 args = parser.parse_args()
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231 df = pd.read_csv(args.input_tab, sep='\t')
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232 NCOLS = df.columns.size
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233 MAXLEN = 30 # tricky way to truncate long axis tickmarks
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234 defaultcols = ['col%d' % (x+1) for x in range(NCOLS)]
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235 if len(args.header.strip()) > 0:
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236 newcols = args.header.split(',')
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237 if len(newcols) == NCOLS:
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238 df.columns = newcols
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239 else:
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240 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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241 df.columns = defaultcols
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242 else:
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243 df.columns = defaultcols
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244 df['evalue'] = [-math.log(x + 1e-308) for x in df['evalue']] # convert so large values reflect statistical surprise
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245 if len(args.colourcol.strip()) == 0:
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246 fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol)
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247 else:
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248 fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol)
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249 if args.title:
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250 ftitle=dict(text=args.title, font=dict(size=40))
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251 fig.update_layout(title=ftitle)
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252 for scatter in fig.data:
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253 scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']]
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254 scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']]
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255 if len(args.colourcol.strip()) == 0:
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256 sl = str(scatter['legendgroup'])
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257 if len(sl) > MAXLEN:
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258 scatter['legendgroup'] = sl[:MAXLEN]
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259 if args.image_type == "short_html":
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260 fig.write_html(args.htmlout, full_html=False, include_plotlyjs='cdn')
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261 elif args.image_type == "long_html":
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262 fig.write_html(args.htmlout)
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263 elif args.image_type == "small_png":
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264 ht = 768
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265 wdth = 1024
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266 fig.write_image('plotly.png', height=ht, width=wdth)
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267 shutil.copyfile('plotly.png', args.htmlout)
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268 else:
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269 ht = 1200
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270 wdth = 1920
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271 fig.write_image('plotly.png', height=ht, width=wdth)
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272 shutil.copyfile('plotly.png', args.htmlout)
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273
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274 ]]></help>
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275 <citations>
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276 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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277 </citations>
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278 </tool>
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279
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