|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_feature-table_heatmap" name="qiime feature-table heatmap"
|
|
|
3 version="2020.8">
|
|
|
4 <description>Generate a heatmap representation of a feature table</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command><![CDATA[
|
|
|
9 qiime feature-table heatmap
|
|
|
10
|
|
|
11 --i-table=$itable
|
|
|
12 # if $input_files_msamplemetadatafile:
|
|
|
13 # def list_dict_to_string(list_dict):
|
|
|
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
15 # for d in list_dict[1:]:
|
|
|
16 # set $file_list = $file_list + ' --m-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
|
|
|
17 # end for
|
|
|
18 # return $file_list
|
|
|
19 # end def
|
|
|
20 --m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
|
|
|
21 # end if
|
|
|
22
|
|
|
23 #if '__ob__' in str($msamplemetadatacolumn):
|
|
|
24 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__ob__', '[')
|
|
|
25 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
|
|
|
26 #end if
|
|
|
27 #if '__cb__' in str($msamplemetadatacolumn):
|
|
|
28 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__cb__', ']')
|
|
|
29 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
|
|
|
30 #end if
|
|
|
31 #if 'X' in str($msamplemetadatacolumn):
|
|
|
32 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('X', '\\')
|
|
|
33 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
|
|
|
34 #end if
|
|
|
35 #if '__sq__' in str($msamplemetadatacolumn):
|
|
|
36 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__sq__', "'")
|
|
|
37 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
|
|
|
38 #end if
|
|
|
39 #if '__db__' in str($msamplemetadatacolumn):
|
|
|
40 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__db__', '"')
|
|
|
41 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
|
|
|
42 #end if
|
|
|
43
|
|
|
44 #if str($msamplemetadatacolumn):
|
|
|
45 --m-sample-metadata-column=$msamplemetadatacolumn
|
|
|
46 #end if
|
|
|
47 # if $input_files_mfeaturemetadatafile:
|
|
|
48 # def list_dict_to_string(list_dict):
|
|
|
49 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
50 # for d in list_dict[1:]:
|
|
|
51 # set $file_list = $file_list + ' --m-feature-metadata-file=' + d['additional_input'].__getattr__('file_name')
|
|
|
52 # end for
|
|
|
53 # return $file_list
|
|
|
54 # end def
|
|
|
55 --m-feature-metadata-file=$list_dict_to_string($input_files_mfeaturemetadatafile)
|
|
|
56 # end if
|
|
|
57
|
|
|
58 #if '__ob__' in str($mfeaturemetadatacolumn):
|
|
|
59 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__ob__', '[')
|
|
|
60 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
|
|
|
61 #end if
|
|
|
62 #if '__cb__' in str($mfeaturemetadatacolumn):
|
|
|
63 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__cb__', ']')
|
|
|
64 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
|
|
|
65 #end if
|
|
|
66 #if 'X' in str($mfeaturemetadatacolumn):
|
|
|
67 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('X', '\\')
|
|
|
68 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
|
|
|
69 #end if
|
|
|
70 #if '__sq__' in str($mfeaturemetadatacolumn):
|
|
|
71 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__sq__', "'")
|
|
|
72 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
|
|
|
73 #end if
|
|
|
74 #if '__db__' in str($mfeaturemetadatacolumn):
|
|
|
75 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__db__', '"')
|
|
|
76 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
|
|
|
77 #end if
|
|
|
78
|
|
|
79 #if str($mfeaturemetadatacolumn):
|
|
|
80 --m-feature-metadata-column=$mfeaturemetadatacolumn
|
|
|
81 #end if
|
|
|
82
|
|
|
83 #if $pnonormalize:
|
|
|
84 --p-no-normalize
|
|
|
85 #end if
|
|
|
86
|
|
|
87 #if str($ptitle):
|
|
|
88 --p-title=$ptitle
|
|
|
89 #end if
|
|
|
90 #if str($pmetric) != 'None':
|
|
|
91 --p-metric=$pmetric
|
|
|
92 #end if
|
|
|
93
|
|
|
94 #if str($pmethod) != 'None':
|
|
|
95 --p-method=$pmethod
|
|
|
96 #end if
|
|
|
97
|
|
|
98 #if str($pcluster) != 'None':
|
|
|
99 --p-cluster=$pcluster
|
|
|
100 #end if
|
|
|
101
|
|
|
102 #if str($pcolorscheme) != 'None':
|
|
|
103 --p-color-scheme=$pcolorscheme
|
|
|
104 #end if
|
|
|
105
|
|
|
106 --o-visualization=ovisualization
|
|
|
107
|
|
|
108 #if str($examples) != 'None':
|
|
|
109 --examples=$examples
|
|
|
110 #end if
|
|
|
111
|
|
|
112 ;
|
|
|
113 cp ogroupedtable.qza $ogroupedtable
|
|
|
114
|
|
|
115 ;
|
|
|
116 qiime tools export ovisualization.qzv --output-path out
|
|
|
117 && mkdir -p '$ovisualization.files_path'
|
|
|
118 && cp -r out/* '$ovisualization.files_path'
|
|
|
119 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
|
120
|
|
|
121 ]]></command>
|
|
|
122 <inputs>
|
|
|
123 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to visualize. [required]" name="itable" optional="False" type="data" />
|
|
|
124 <repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
|
|
|
125 <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
|
|
|
126 </repeat>
|
|
|
127 <param label="--m-sample-metadata-column: COLUMN MetadataColumn[Categorical] Annotate the sample IDs with these sample metadata values. When metadata is present and `cluster`=\'feature\', samples will be sorted by the metadata values. [optional]" name="msamplemetadatacolumn" optional="False" type="text" />
|
|
|
128 <repeat name="input_files_mfeaturemetadatafile" optional="True" title="--m-feature-metadata-file">
|
|
|
129 <param format="tabular,qza,no_unzip.zip" label="--m-feature-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
|
|
|
130 </repeat>
|
|
|
131 <param label="--m-feature-metadata-column: COLUMN MetadataColumn[Categorical] Annotate the feature IDs with these feature metadata values. When metadata is present and `cluster`=\'sample\', features will be sorted by the metadata values. [optional]" name="mfeaturemetadatacolumn" optional="False" type="text" />
|
|
|
132 <param label="--p-no-normalize: Do not normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table. [default: True]" name="pnonormalize" selected="False" type="boolean" />
|
|
|
133 <param label="--p-title: TEXT Optional custom plot title. [optional]" name="ptitle" optional="False" type="text" />
|
|
|
134 <param label="--p-metric: " name="pmetric" optional="True" type="select">
|
|
|
135 <option selected="True" value="None">Selection is Optional</option>
|
|
|
136 <option value="euclidean">euclidean</option>
|
|
|
137 <option value="cityblock">cityblock</option>
|
|
|
138 <option value="matching">matching</option>
|
|
|
139 <option value="russellrao">russellrao</option>
|
|
|
140 <option value="sokalmichener">sokalmichener</option>
|
|
|
141 <option value="kulsinski">kulsinski</option>
|
|
|
142 <option value="chebyshev">chebyshev</option>
|
|
|
143 <option value="hamming">hamming</option>
|
|
|
144 <option value="dice">dice</option>
|
|
|
145 <option value="yule">yule</option>
|
|
|
146 <option value="rogerstanimoto">rogerstanimoto</option>
|
|
|
147 <option value="braycurtis">braycurtis</option>
|
|
|
148 <option value="cosine">cosine</option>
|
|
|
149 <option value="minkowski">minkowski</option>
|
|
|
150 <option value="correlation">correlation</option>
|
|
|
151 <option value="sokalsneath">sokalsneath</option>
|
|
|
152 <option value="seuclidean">seuclidean</option>
|
|
|
153 <option value="canberra">canberra</option>
|
|
|
154 <option value="mahalanobis">mahalanobis</option>
|
|
|
155 <option value="jaccard">jaccard</option>
|
|
|
156 <option value="sqeuclidean">sqeuclidean</option>
|
|
|
157 </param>
|
|
|
158 <param label="--p-method: " name="pmethod" optional="True" type="select">
|
|
|
159 <option selected="True" value="None">Selection is Optional</option>
|
|
|
160 <option value="centroid">centroid</option>
|
|
|
161 <option value="median">median</option>
|
|
|
162 <option value="weighted">weighted</option>
|
|
|
163 <option value="average">average</option>
|
|
|
164 <option value="single">single</option>
|
|
|
165 <option value="complete">complete</option>
|
|
|
166 <option value="ward">ward</option>
|
|
|
167 </param>
|
|
|
168 <param label="--p-cluster: " name="pcluster" optional="True" type="select">
|
|
|
169 <option selected="True" value="None">Selection is Optional</option>
|
|
|
170 <option value="both">both</option>
|
|
|
171 <option value="none">none</option>
|
|
|
172 <option value="features">features</option>
|
|
|
173 <option value="samples">samples</option>
|
|
|
174 </param>
|
|
|
175 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
|
|
|
176 <option selected="True" value="None">Selection is Optional</option>
|
|
|
177 <option value="Spectral">Spectral</option>
|
|
|
178 <option value="flag">flag</option>
|
|
|
179 <option value="jet">jet</option>
|
|
|
180 <option value="Vega20">Vega20</option>
|
|
|
181 <option value="terrain">terrain</option>
|
|
|
182 <option value="jet_r">jet_r</option>
|
|
|
183 <option value="Vega20c_r">Vega20c_r</option>
|
|
|
184 <option value="Oranges_r">Oranges_r</option>
|
|
|
185 <option value="spectral">spectral</option>
|
|
|
186 <option value="summer">summer</option>
|
|
|
187 <option value="BuPu_r">BuPu_r</option>
|
|
|
188 <option value="tab20b_r">tab20b_r</option>
|
|
|
189 <option value="Pastel1">Pastel1</option>
|
|
|
190 <option value="gnuplot_r">gnuplot_r</option>
|
|
|
191 <option value="seismic">seismic</option>
|
|
|
192 <option value="icefire">icefire</option>
|
|
|
193 <option value="Set1">Set1</option>
|
|
|
194 <option value="bwr">bwr</option>
|
|
|
195 <option value="coolwarm_r">coolwarm_r</option>
|
|
|
196 <option value="ocean_r">ocean_r</option>
|
|
|
197 <option value="gist_gray_r">gist_gray_r</option>
|
|
|
198 <option value="autumn">autumn</option>
|
|
|
199 <option value="BrBG">BrBG</option>
|
|
|
200 <option value="Pastel2">Pastel2</option>
|
|
|
201 <option value="GnBu">GnBu</option>
|
|
|
202 <option value="Vega20b_r">Vega20b_r</option>
|
|
|
203 <option value="tab20c">tab20c</option>
|
|
|
204 <option value="Paired">Paired</option>
|
|
|
205 <option value="YlOrRd_r">YlOrRd_r</option>
|
|
|
206 <option value="icefire_r">icefire_r</option>
|
|
|
207 <option value="cubehelix_r">cubehelix_r</option>
|
|
|
208 <option value="CMRmap_r">CMRmap_r</option>
|
|
|
209 <option value="RdBu">RdBu</option>
|
|
|
210 <option value="YlGn_r">YlGn_r</option>
|
|
|
211 <option value="gray_r">gray_r</option>
|
|
|
212 <option value="mako_r">mako_r</option>
|
|
|
213 <option value="OrRd_r">OrRd_r</option>
|
|
|
214 <option value="Vega10">Vega10</option>
|
|
|
215 <option value="Set3">Set3</option>
|
|
|
216 <option value="RdYlGn_r">RdYlGn_r</option>
|
|
|
217 <option value="hsv">hsv</option>
|
|
|
218 <option value="cool_r">cool_r</option>
|
|
|
219 <option value="Spectral_r">Spectral_r</option>
|
|
|
220 <option value="rainbow">rainbow</option>
|
|
|
221 <option value="cividis">cividis</option>
|
|
|
222 <option value="Blues_r">Blues_r</option>
|
|
|
223 <option value="PuOr_r">PuOr_r</option>
|
|
|
224 <option value="binary_r">binary_r</option>
|
|
|
225 <option value="RdGy">RdGy</option>
|
|
|
226 <option value="Pastel2_r">Pastel2_r</option>
|
|
|
227 <option value="Pastel1_r">Pastel1_r</option>
|
|
|
228 <option value="Dark2">Dark2</option>
|
|
|
229 <option value="vlag">vlag</option>
|
|
|
230 <option value="binary">binary</option>
|
|
|
231 <option value="pink">pink</option>
|
|
|
232 <option value="Purples">Purples</option>
|
|
|
233 <option value="cividis_r">cividis_r</option>
|
|
|
234 <option value="gray">gray</option>
|
|
|
235 <option value="seismic_r">seismic_r</option>
|
|
|
236 <option value="Greys">Greys</option>
|
|
|
237 <option value="tab20">tab20</option>
|
|
|
238 <option value="BuPu">BuPu</option>
|
|
|
239 <option value="RdBu_r">RdBu_r</option>
|
|
|
240 <option value="gnuplot2_r">gnuplot2_r</option>
|
|
|
241 <option value="Accent_r">Accent_r</option>
|
|
|
242 <option value="magma">magma</option>
|
|
|
243 <option value="copper_r">copper_r</option>
|
|
|
244 <option value="inferno">inferno</option>
|
|
|
245 <option value="nipy_spectral_r">nipy_spectral_r</option>
|
|
|
246 <option value="pink_r">pink_r</option>
|
|
|
247 <option value="copper">copper</option>
|
|
|
248 <option value="Dark2_r">Dark2_r</option>
|
|
|
249 <option value="YlGnBu_r">YlGnBu_r</option>
|
|
|
250 <option value="Wistia_r">Wistia_r</option>
|
|
|
251 <option value="spectral_r">spectral_r</option>
|
|
|
252 <option value="cubehelix">cubehelix</option>
|
|
|
253 <option value="tab20_r">tab20_r</option>
|
|
|
254 <option value="viridis">viridis</option>
|
|
|
255 <option value="RdYlBu">RdYlBu</option>
|
|
|
256 <option value="Blues">Blues</option>
|
|
|
257 <option value="rocket_r">rocket_r</option>
|
|
|
258 <option value="Set1_r">Set1_r</option>
|
|
|
259 <option value="brg_r">brg_r</option>
|
|
|
260 <option value="bone_r">bone_r</option>
|
|
|
261 <option value="gist_ncar_r">gist_ncar_r</option>
|
|
|
262 <option value="afmhot">afmhot</option>
|
|
|
263 <option value="RdYlBu_r">RdYlBu_r</option>
|
|
|
264 <option value="gist_earth_r">gist_earth_r</option>
|
|
|
265 <option value="RdGy_r">RdGy_r</option>
|
|
|
266 <option value="Vega10_r">Vega10_r</option>
|
|
|
267 <option value="gist_rainbow_r">gist_rainbow_r</option>
|
|
|
268 <option value="spring">spring</option>
|
|
|
269 <option value="Set3_r">Set3_r</option>
|
|
|
270 <option value="magma_r">magma_r</option>
|
|
|
271 <option value="mako">mako</option>
|
|
|
272 <option value="PuRd">PuRd</option>
|
|
|
273 <option value="gnuplot2">gnuplot2</option>
|
|
|
274 <option value="Paired_r">Paired_r</option>
|
|
|
275 <option value="Vega20b">Vega20b</option>
|
|
|
276 <option value="Accent">Accent</option>
|
|
|
277 <option value="hsv_r">hsv_r</option>
|
|
|
278 <option value="ocean">ocean</option>
|
|
|
279 <option value="gist_earth">gist_earth</option>
|
|
|
280 <option value="afmhot_r">afmhot_r</option>
|
|
|
281 <option value="bone">bone</option>
|
|
|
282 <option value="rocket">rocket</option>
|
|
|
283 <option value="RdYlGn">RdYlGn</option>
|
|
|
284 <option value="bwr_r">bwr_r</option>
|
|
|
285 <option value="RdPu_r">RdPu_r</option>
|
|
|
286 <option value="BuGn">BuGn</option>
|
|
|
287 <option value="PuBu">PuBu</option>
|
|
|
288 <option value="hot_r">hot_r</option>
|
|
|
289 <option value="Vega20c">Vega20c</option>
|
|
|
290 <option value="gist_yarg">gist_yarg</option>
|
|
|
291 <option value="tab10">tab10</option>
|
|
|
292 <option value="coolwarm">coolwarm</option>
|
|
|
293 <option value="winter_r">winter_r</option>
|
|
|
294 <option value="plasma_r">plasma_r</option>
|
|
|
295 <option value="Wistia">Wistia</option>
|
|
|
296 <option value="BuGn_r">BuGn_r</option>
|
|
|
297 <option value="Set2">Set2</option>
|
|
|
298 <option value="Vega20_r">Vega20_r</option>
|
|
|
299 <option value="hot">hot</option>
|
|
|
300 <option value="brg">brg</option>
|
|
|
301 <option value="BrBG_r">BrBG_r</option>
|
|
|
302 <option value="gist_heat">gist_heat</option>
|
|
|
303 <option value="YlOrRd">YlOrRd</option>
|
|
|
304 <option value="inferno_r">inferno_r</option>
|
|
|
305 <option value="viridis_r">viridis_r</option>
|
|
|
306 <option value="gist_stern_r">gist_stern_r</option>
|
|
|
307 <option value="tab20c_r">tab20c_r</option>
|
|
|
308 <option value="gist_gray">gist_gray</option>
|
|
|
309 <option value="Reds_r">Reds_r</option>
|
|
|
310 <option value="flag_r">flag_r</option>
|
|
|
311 <option value="Purples_r">Purples_r</option>
|
|
|
312 <option value="vlag_r">vlag_r</option>
|
|
|
313 <option value="summer_r">summer_r</option>
|
|
|
314 <option value="Greys_r">Greys_r</option>
|
|
|
315 <option value="PRGn">PRGn</option>
|
|
|
316 <option value="PiYG">PiYG</option>
|
|
|
317 <option value="gist_ncar">gist_ncar</option>
|
|
|
318 <option value="Oranges">Oranges</option>
|
|
|
319 <option value="Reds">Reds</option>
|
|
|
320 <option value="GnBu_r">GnBu_r</option>
|
|
|
321 <option value="RdPu">RdPu</option>
|
|
|
322 <option value="YlOrBr_r">YlOrBr_r</option>
|
|
|
323 <option value="autumn_r">autumn_r</option>
|
|
|
324 <option value="YlGn">YlGn</option>
|
|
|
325 <option value="CMRmap">CMRmap</option>
|
|
|
326 <option value="gnuplot">gnuplot</option>
|
|
|
327 <option value="rainbow_r">rainbow_r</option>
|
|
|
328 <option value="PiYG_r">PiYG_r</option>
|
|
|
329 <option value="Greens">Greens</option>
|
|
|
330 <option value="YlOrBr">YlOrBr</option>
|
|
|
331 <option value="prism_r">prism_r</option>
|
|
|
332 <option value="winter">winter</option>
|
|
|
333 <option value="gist_yarg_r">gist_yarg_r</option>
|
|
|
334 <option value="Set2_r">Set2_r</option>
|
|
|
335 <option value="nipy_spectral">nipy_spectral</option>
|
|
|
336 <option value="plasma">plasma</option>
|
|
|
337 <option value="OrRd">OrRd</option>
|
|
|
338 <option value="Greens_r">Greens_r</option>
|
|
|
339 <option value="tab10_r">tab10_r</option>
|
|
|
340 <option value="YlGnBu">YlGnBu</option>
|
|
|
341 <option value="prism">prism</option>
|
|
|
342 <option value="PRGn_r">PRGn_r</option>
|
|
|
343 <option value="gist_heat_r">gist_heat_r</option>
|
|
|
344 <option value="terrain_r">terrain_r</option>
|
|
|
345 <option value="tab20b">tab20b</option>
|
|
|
346 <option value="PuBuGn">PuBuGn</option>
|
|
|
347 <option value="PuBu_r">PuBu_r</option>
|
|
|
348 <option value="spring_r">spring_r</option>
|
|
|
349 <option value="gist_rainbow">gist_rainbow</option>
|
|
|
350 <option value="cool">cool</option>
|
|
|
351 <option value="PuOr">PuOr</option>
|
|
|
352 <option value="PuRd_r">PuRd_r</option>
|
|
|
353 <option value="gist_stern">gist_stern</option>
|
|
|
354 <option value="PuBuGn_r">PuBuGn_r</option>
|
|
|
355 </param>
|
|
|
356 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
|
357
|
|
|
358 </inputs>
|
|
|
359
|
|
|
360 <outputs>
|
|
|
361 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
|
|
|
362
|
|
|
363 </outputs>
|
|
|
364
|
|
|
365 <help><![CDATA[
|
|
|
366 Generate a heatmap representation of a feature table
|
|
|
367 ###############################################################
|
|
|
368
|
|
|
369 Generate a heatmap representation of a feature table with optional
|
|
|
370 clustering on both the sample and feature axes. Tip: To generate a heatmap
|
|
|
371 containing taxonomic annotations, use `qiime taxa collapse` to collapse the
|
|
|
372 feature table at the desired taxonomic level.
|
|
|
373
|
|
|
374 Parameters
|
|
|
375 ----------
|
|
|
376 table : FeatureTable[Frequency]
|
|
|
377 The feature table to visualize.
|
|
|
378 sample_metadata : MetadataColumn[Categorical], optional
|
|
|
379 Annotate the sample IDs with these sample metadata values. When
|
|
|
380 metadata is present and `cluster`='feature', samples will be sorted by
|
|
|
381 the metadata values.
|
|
|
382 feature_metadata : MetadataColumn[Categorical], optional
|
|
|
383 Annotate the feature IDs with these feature metadata values. When
|
|
|
384 metadata is present and `cluster`='sample', features will be sorted by
|
|
|
385 the metadata values.
|
|
|
386 normalize : Bool, optional
|
|
|
387 Normalize the feature table by adding a psuedocount of 1 and then
|
|
|
388 taking the log10 of the table.
|
|
|
389 title : Str, optional
|
|
|
390 Optional custom plot title.
|
|
|
391 metric : Str % Choices('yule', 'seuclidean', 'sokalmichener', 'sokalsneath', 'hamming', 'canberra', 'cityblock', 'russellrao', 'jaccard', 'braycurtis', 'minkowski', 'euclidean', 'kulsinski', 'cosine', 'sqeuclidean', 'correlation', 'dice', 'rogerstanimoto', 'mahalanobis', 'chebyshev', 'matching'), optional
|
|
|
392 Metrics exposed by seaborn (see http://seaborn.pydata.org/generated/sea
|
|
|
393 born.clustermap.html#seaborn.clustermap for more detail).
|
|
|
394 method : Str % Choices('complete', 'average', 'ward', 'median', 'weighted', 'centroid', 'single'), optional
|
|
|
395 Clustering methods exposed by seaborn (see http://seaborn.pydata.org/ge
|
|
|
396 nerated/seaborn.clustermap.html#seaborn.clustermap for more detail).
|
|
|
397 cluster : Str % Choices('both', 'features', 'none', 'samples'), optional
|
|
|
398 Specify which axes to cluster.
|
|
|
399 color_scheme : Str % Choices('YlGn', 'flag', 'Greens_r', 'RdPu_r', 'OrRd', 'Set1_r', 'RdYlGn', 'inferno_r', 'Accent_r', 'bwr', 'PuOr', 'seismic_r', 'RdGy_r', 'tab20b_r', 'Oranges', 'spectral', 'RdYlGn_r', 'nipy_spectral_r', 'gist_gray', 'binary', 'gist_yarg_r', 'cubehelix', 'viridis_r', 'autumn', 'bone_r', 'terrain_r', 'RdPu', 'inferno', 'PRGn', 'YlGnBu', 'mako', 'gray', 'tab20_r', 'Oranges_r', 'gist_stern_r', 'Dark2_r', 'Purples_r', 'coolwarm', 'RdYlBu', 'tab10', 'copper_r', 'YlOrRd_r', 'gray_r', 'magma', 'Set3_r', 'BuGn', 'viridis', 'icefire_r', 'PuOr_r', 'YlOrBr', 'winter_r', 'hsv', 'gist_earth_r', 'rocket_r', 'Vega20b', 'autumn_r', 'gnuplot', 'Paired', 'PuRd_r', 'BrBG_r', 'plasma_r', 'Set2', 'prism', 'winter', 'seismic', 'RdGy', 'Blues_r', 'Reds_r', 'gist_ncar_r', 'Reds', 'afmhot', 'Greys', 'rainbow', 'tab10_r', 'GnBu_r', 'gnuplot2', 'pink', 'tab20b', 'BuGn_r', 'PuRd', 'gist_stern', 'magma_r', 'prism_r', 'tab20c_r', 'BuPu', 'cividis_r', 'BrBG', 'Wistia_r', 'gist_gray_r', 'ocean_r', 'summer_r', 'mako_r', 'CMRmap_r', 'cool_r', 'coolwarm_r', 'Greens', 'RdBu', 'icefire', 'spectral_r', 'Vega20', 'brg', 'Paired_r', 'BuPu_r', 'gist_rainbow', 'CMRmap', 'cool', 'gist_earth', 'bwr_r', 'rocket', 'YlGn_r', 'Vega20b_r', 'Wistia', 'Vega20c_r', 'Accent', 'plasma', 'Set1', 'PuBu_r', 'Purples', 'RdYlBu_r', 'brg_r', 'flag_r', 'Set3', 'hot_r', 'Blues', 'Pastel1_r', 'YlOrBr_r', 'hsv_r', 'Pastel2', 'Pastel1', 'bone', 'tab20', 'PuBuGn_r', 'terrain', 'gist_rainbow_r', 'Spectral_r', 'Pastel2_r', 'RdBu_r', 'summer', 'gist_ncar', 'OrRd_r', 'copper', 'tab20c', 'PuBuGn', 'Set2_r', 'vlag', 'jet_r', 'gist_heat_r', 'PRGn_r', 'Vega10', 'jet', 'Spectral', 'rainbow_r', 'binary_r', 'ocean', 'spring', 'Dark2', 'Vega20_r', 'vlag_r', 'PiYG', 'PuBu', 'YlGnBu_r', 'afmhot_r', 'nipy_spectral', 'gnuplot2_r', 'cividis', 'gnuplot_r', 'Greys_r', 'cubehelix_r', 'spring_r', 'PiYG_r', 'gist_yarg', 'gist_heat', 'Vega20c', 'GnBu', 'YlOrRd', 'hot', 'Vega10_r', 'pink_r'), optional
|
|
|
400 The matplotlib colorscheme to generate the heatmap with.
|
|
|
401
|
|
|
402 Returns
|
|
|
403 -------
|
|
|
404 visualization : Visualization
|
|
|
405 ]]></help>
|
|
|
406 <macros>
|
|
|
407 <import>qiime_citation.xml</import>
|
|
|
408 </macros>
|
|
|
409 <expand macro="qiime_citation"/>
|
|
|
410 </tool> |
