Mercurial > repos > fubar > plotly_blast_plot

comparison plotly_blast_tool/plotlyblast.xml @ 2:47a7eeec4a19 draft

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author fubar
date Wed, 26 Jul 2023 12:16:56 +0000
parents 6fbd48e9c950
children 82bcfcb60f97
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1:6fbd48e9c950 2:47a7eeec4a19
1 <tool name="plotlyblast" id="plotlyblast" version="3.0"> 1 <tool name="plotlyblast" id="plotlyblast" version="3.0">
2 <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay--> 2 <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
3 <!--Created by toolfactory@galaxy.org at 26/07/2023 15:45:12 using the Galaxy Tool Factory.--> 3 <!--Created by toolfactory@galaxy.org at 26/07/2023 17:31:09 using the Galaxy Tool Factory.-->
4 <description>Plotly plot generator</description> 4 <description>Plotly plot generator</description>
5 <requirements> 5 <requirements>
6 <requirement type="package">pandas</requirement> 6 <requirement type="package" version="1.5.3">pandas</requirement>
7 <requirement type="package">plotly</requirement> 7 <requirement type="package" version="5.9.0">plotly</requirement>
8 </requirements> 8 </requirements>
9 <stdio> 9 <stdio>
10 <exit_code range="1:" level="fatal"/> 10 <exit_code range="1:" level="fatal"/>
11 </stdio> 11 </stdio>
12 <version_command><![CDATA[echo "3.0"]]></version_command> 12 <version_command><![CDATA[echo "3.0"]]></version_command>
42 parser = argparse.ArgumentParser() 42 parser = argparse.ArgumentParser()
43 a = parser.add_argument 43 a = parser.add_argument
44 a('--input_tab',default='') 44 a('--input_tab',default='')
45 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') 45 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')
46 a('--htmlout',default="test_run.html") 46 a('--htmlout',default="test_run.html")
47 a('--xcol',default='gaps') 47 a('--xcol',default='')
48 a('--ycol',default='qseq') 48 a('--ycol',default='')
49 a('--colourcol',default='qaccver') 49 a('--colourcol',default='')
50 a('--hovercol',default='qseq') 50 a('--hovercol',default='')
51 a('--title',default='test blast plot of mismatch by bitscore coloured by qaccver ') 51 a('--title',default='test blast plot')
52 args = parser.parse_args() 52 args = parser.parse_args()
53 df = pd.read_csv(args.input_tab, sep='\t') 53 df = pd.read_csv(args.input_tab, sep='\t')
54 NCOLS = df.columns.size 54 NCOLS = df.columns.size
55 MAXLEN = 30 # tricky way to truncate long axis tickmarks 55 MAXLEN = 30 # tricky way to truncate long axis tickmarks
56 defaultcols = ['col%d' % (x+1) for x in range(NCOLS)] 56 defaultcols = ['col%d' % (x+1) for x in range(NCOLS)]
67 if len(args.colourcol.strip()) == 0: 67 if len(args.colourcol.strip()) == 0:
68 fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol) 68 fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol)
69 else: 69 else:
70 fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol) 70 fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol)
71 if args.title: 71 if args.title:
72 ftitle=dict(text=args.title, font=dict(size=40), automargin=True) 72 fig.update_layout(title=dict(text=args.title, font=dict(size=40)))
73 fig.update_layout(title=ftitle) 73
74
74 for scatter in fig.data: 75 for scatter in fig.data:
75 scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']] 76 scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']]
76 scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']] 77 scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']]
77 if len(args.colourcol.strip()) == 0: 78 if len(args.colourcol.strip()) == 0:
78 sl = str(scatter['legendgroup']) 79 sl = str(scatter['legendgroup'])
127 128
128 ---- 129 ----
129 130
130 131
131 132
132 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. 133 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.
133 134
134 135
135 136
136 Assumes you want a hover display for an interactive plot to be informative 137 Assumes you want a hover display for an interactive plot to be informative
137 138
161 162
162 :height: 400 163 :height: 400
163 164
164 :width: 400 165 :width: 400
165 166
166 167
167 168
168 ------ 169 ------
169 170
170 171
171 Script:: 172 Script::
181 parser = argparse.ArgumentParser() 182 parser = argparse.ArgumentParser()
182 a = parser.add_argument 183 a = parser.add_argument
183 a('--input_tab',default='') 184 a('--input_tab',default='')
184 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') 185 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')
185 a('--htmlout',default="test_run.html") 186 a('--htmlout',default="test_run.html")
186 a('--xcol',default='gaps') 187 a('--xcol',default='')
187 a('--ycol',default='qseq') 188 a('--ycol',default='')
188 a('--colourcol',default='qaccver') 189 a('--colourcol',default='')
189 a('--hovercol',default='qseq') 190 a('--hovercol',default='')
190 a('--title',default='test blast plot of mismatch by bitscore coloured by qaccver ') 191 a('--title',default='test blast plot')
191 args = parser.parse_args() 192 args = parser.parse_args()
192 df = pd.read_csv(args.input_tab, sep='\t') 193 df = pd.read_csv(args.input_tab, sep='\t')
193 NCOLS = df.columns.size 194 NCOLS = df.columns.size
194 MAXLEN = 30 # tricky way to truncate long axis tickmarks 195 MAXLEN = 30 # tricky way to truncate long axis tickmarks
195 defaultcols = ['col%d' % (x+1) for x in range(NCOLS)] 196 defaultcols = ['col%d' % (x+1) for x in range(NCOLS)]