Mercurial > repos > fubar > plotly_blast_plot
annotate plotly_blast_tool/plotlyblast.xml @ 3:82bcfcb60f97 draft default tip
Updated by re-generating with latest ToolFactory so png or html outputs can be requested. Output labels are informative too.
| author | fubar |
|---|---|
| date | Fri, 04 Aug 2023 01:55:07 +0000 |
| parents | 47a7eeec4a19 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool name="plotlyblast" id="plotlyblast" version="3.0"> |
| 1 | 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> |
| 0 | 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> |
| 0 | 9 </requirements> |
| 10 <stdio> | |
| 11 <exit_code range="1:" level="fatal"/> | |
| 12 </stdio> | |
| 13 <version_command><![CDATA[echo "3.0"]]></version_command> | |
| 14 <command><![CDATA[python | |
| 15 $runme | |
| 16 --input_tab | |
| 17 $input_tab | |
| 18 --htmlout | |
| 19 $htmlout | |
| 20 --xcol | |
| 21 "$xcol" | |
| 22 --ycol | |
| 23 "$ycol" | |
| 24 --colourcol | |
| 25 "$colourcol" | |
| 26 --hovercol | |
| 27 "$hovercol" | |
| 28 --title | |
| 29 "$title" | |
| 30 --header | |
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31 "$header" |
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32 --image_type |
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33 "$outputimagetype"]]></command> |
| 0 | 34 <configfiles> |
| 35 <configfile name="runme"><![CDATA[#raw | |
| 36 | |
| 37 import argparse | |
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38 import shutil |
| 0 | 39 import sys |
| 40 import math | |
| 41 import plotly.express as px | |
| 42 import pandas as pd | |
| 43 # Ross Lazarus July 2023 | |
| 44 # based on various plotly tutorials | |
| 45 # Expects a blastn search result passed in as the first command line parameter. | |
| 46 parser = argparse.ArgumentParser() | |
| 47 a = parser.add_argument | |
| 48 a('--input_tab',default='') | |
| 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') | |
| 50 a('--htmlout',default="test_run.html") | |
| 2 | 51 a('--xcol',default='') |
| 52 a('--ycol',default='') | |
| 53 a('--colourcol',default='') | |
| 54 a('--hovercol',default='') | |
| 55 a('--title',default='test blast plot') | |
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56 a('--image_type',default='short_html') |
| 0 | 57 args = parser.parse_args() |
| 58 df = pd.read_csv(args.input_tab, sep='\t') | |
| 59 NCOLS = df.columns.size | |
| 1 | 60 MAXLEN = 30 # tricky way to truncate long axis tickmarks |
| 0 | 61 defaultcols = ['col%d' % (x+1) for x in range(NCOLS)] |
| 62 if len(args.header.strip()) > 0: | |
| 63 newcols = args.header.split(',') | |
| 64 if len(newcols) == NCOLS: | |
| 65 df.columns = newcols | |
| 66 else: | |
| 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)) | |
| 68 df.columns = defaultcols | |
| 69 else: | |
| 70 df.columns = defaultcols | |
| 1 | 71 df['evalue'] = [-math.log(x + 1e-308) for x in df['evalue']] # convert so large values reflect statistical surprise |
| 0 | 72 if len(args.colourcol.strip()) == 0: |
| 73 fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol) | |
| 74 else: | |
| 75 fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol) | |
| 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) |
| 0 | 79 for scatter in fig.data: |
| 80 scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']] | |
| 81 scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']] | |
| 1 | 82 if len(args.colourcol.strip()) == 0: |
| 83 sl = str(scatter['legendgroup']) | |
| 84 if len(sl) > MAXLEN: | |
| 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 |
| 0 | 101 |
| 1 | 102 |
| 0 | 103 #end raw]]></configfile> |
| 104 </configfiles> | |
| 105 <inputs> | |
| 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=""/> |
| 0 | 108 <param name="ycol" type="text" value="bitscore" label="y axis for plot" help=""/> |
| 1 | 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 "/> |
| 0 | 110 <param name="hovercol" type="text" value="qseq" label="columname for hover string" help=""/> |
| 1 | 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"/> |
| 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> |
| 0 | 119 </inputs> |
| 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> |
| 0 | 127 </outputs> |
| 128 <tests> | |
| 129 <test> | |
| 130 <output name="htmlout" value="htmlout_sample" compare="sim_size" delta="5000"/> | |
| 131 <param name="input_tab" value="input_tab_sample"/> | |
| 1 | 132 <param name="xcol" value="qaccver"/> |
| 0 | 133 <param name="ycol" value="bitscore"/> |
| 1 | 134 <param name="colourcol" value="piden"/> |
| 0 | 135 <param name="hovercol" value="qseq"/> |
| 1 | 136 <param name="title" value="Qaccver by bitscore coloured by pident. Hover shows blast match."/> |
| 0 | 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"/> |
| 0 | 139 </test> |
| 140 </tests> | |
| 141 <help><![CDATA[ | |
| 142 | |
| 143 This is a specialised version of a generic tabular file plotter tool plotlytabular | |
| 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 |
| 0 | 155 |
| 156 | |
| 157 .. class:: warningmark | |
| 158 | |
| 1 | 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. |
| 160 | |
| 0 | 161 |
| 162 | |
| 1 | 163 .. class:: warningmark |
| 0 | 164 |
| 1 | 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. |
| 0 | 166 |
| 167 | |
| 168 | |
| 169 ---- | |
| 170 | |
| 171 | |
| 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. |
| 0 | 174 |
| 175 | |
| 176 | |
| 177 Assumes you want a hover display for an interactive plot to be informative | |
| 178 | |
| 179 | |
| 180 | |
| 181 Column names are auto-generated as col1,...coln unless a comma separated list of column names is supplied as the header parameter. | |
| 182 | |
| 183 | |
| 184 | |
| 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. | |
| 186 | |
| 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 | |
| 188 | |
| 189 | |
| 190 | |
| 191 When a header is supplied, the xcol and other column names must match one of those supplied column names. | |
| 192 | |
| 193 So for example, xcol = "qaccver" for the blastn header example rather than xcol = "col1" when no header is supplied. | |
| 194 | |
| 195 | |
| 196 | |
| 197 Relies on Plotly python code released under the MIT licence: https://github.com/plotly/plotly.py/blob/master/LICENSE.txt | |
| 198 | |
| 199 | |
| 200 | |
| 1 | 201 |
| 2 | 202 |
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203 |
| 1 | 204 |
| 0 | 205 ------ |
| 206 | |
| 207 | |
| 208 Script:: | |
| 209 | |
| 210 import argparse | |
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211 import shutil |
| 0 | 212 import sys |
| 213 import math | |
| 214 import plotly.express as px | |
| 215 import pandas as pd | |
| 216 # Ross Lazarus July 2023 | |
| 217 # based on various plotly tutorials | |
| 218 # Expects a blastn search result passed in as the first command line parameter. | |
| 219 parser = argparse.ArgumentParser() | |
| 220 a = parser.add_argument | |
| 221 a('--input_tab',default='') | |
| 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') | |
| 223 a('--htmlout',default="test_run.html") | |
| 2 | 224 a('--xcol',default='') |
| 225 a('--ycol',default='') | |
| 226 a('--colourcol',default='') | |
| 227 a('--hovercol',default='') | |
| 228 a('--title',default='test blast plot') | |
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229 a('--image_type',default='short_html') |
| 0 | 230 args = parser.parse_args() |
| 231 df = pd.read_csv(args.input_tab, sep='\t') | |
| 232 NCOLS = df.columns.size | |
| 1 | 233 MAXLEN = 30 # tricky way to truncate long axis tickmarks |
| 0 | 234 defaultcols = ['col%d' % (x+1) for x in range(NCOLS)] |
| 235 if len(args.header.strip()) > 0: | |
| 236 newcols = args.header.split(',') | |
| 237 if len(newcols) == NCOLS: | |
| 238 df.columns = newcols | |
| 239 else: | |
| 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)) | |
| 241 df.columns = defaultcols | |
| 242 else: | |
| 243 df.columns = defaultcols | |
| 1 | 244 df['evalue'] = [-math.log(x + 1e-308) for x in df['evalue']] # convert so large values reflect statistical surprise |
| 0 | 245 if len(args.colourcol.strip()) == 0: |
| 246 fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol) | |
| 247 else: | |
| 248 fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol) | |
| 249 if args.title: | |
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250 ftitle=dict(text=args.title, font=dict(size=40)) |
| 0 | 251 fig.update_layout(title=ftitle) |
| 252 for scatter in fig.data: | |
| 253 scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']] | |
| 254 scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']] | |
| 1 | 255 if len(args.colourcol.strip()) == 0: |
| 256 sl = str(scatter['legendgroup']) | |
| 257 if len(sl) > MAXLEN: | |
| 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) |
| 0 | 273 |
| 274 ]]></help> | |
| 275 <citations> | |
| 276 <citation type="doi">10.1093/bioinformatics/bts573</citation> | |
| 277 </citations> | |
| 278 </tool> | |
| 279 |