Mercurial > repos > iuc > scanpy_normalize

comparison normalize.xml @ 1:a9f14e2d1655 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
author iuc
date Wed, 16 Oct 2019 06:31:10 -0400
parents ed64c90a9b93
children 8e0f141c8c66
comparison
equal deleted inserted replaced
0:ed64c90a9b93 1:a9f14e2d1655
1 <tool id="scanpy_normalize" name="Normalize with scanpy" version="@galaxy_version@"> 1 <tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@">
2 <description></description> 2 <description>with scanpy</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="version_command"/> 7 <expand macro="version_command"/>
11 <configfiles> 11 <configfiles>
12 <configfile name="script_file"><![CDATA[ 12 <configfile name="script_file"><![CDATA[
13 @CMD_imports@ 13 @CMD_imports@
14 @CMD_read_inputs@ 14 @CMD_read_inputs@
15 15
16 #if $method.method == "pp.normalize_per_cell" 16 #if $method.method == "pp.normalize_total"
17 sc.pp.normalize_per_cell( 17 sc.pp.normalize_total(
18 data=adata, 18 adata,
19 #if $method.counts_per_cell_after 19 #if str($method.target_sum)!= ''
20 counts_per_cell_after=$method.counts_per_cell_after, 20 target_sum=$method.target_sum,
21 #end if 21 #end if
22 #if $method.counts_per_cell 22 exclude_highly_expressed=$method.exclude_highly_expressed.exclude_highly_expressed,
23 counts_per_cell=np.loadtxt('$method.counts_per_cell'), 23 #if $method.exclude_highly_expressed.exclude_highly_expressed == "True"
24 #end if 24 max_fraction=$method.exclude_highly_expressed.max_fraction,
25 key_n_counts='$method.key_n_counts', 25 #end if
26 copy=False) 26 key_added='$method.key_added',
27 adata.obs.to_csv('$anndata_obs', sep='\t') 27 #if str($method.layers) != 'all'
28 #elif $method.method == "pp.recipe_zheng17" 28 layers[str(x.strip()) for x in str($method.layers).split(',')],
29 #else
30 layers='$method.layers',
31 #end if
32 #if str($method.layer_norm) != "None"
33 layer_norm='$method.layer_norm',
34 #end if
35 inplace=True)
36
37 #else if $method.method == "pp.recipe_zheng17"
29 sc.pp.recipe_zheng17( 38 sc.pp.recipe_zheng17(
30 adata=adata, 39 adata=adata,
31 n_top_genes=$method.n_top_genes, 40 n_top_genes=$method.n_top_genes,
32 log=$method.log, 41 log=$method.log,
33 plot=False, 42 plot=False,
34 copy=False) 43 copy=False)
35 #elif $method.method == "pp.recipe_weinreb17" 44
45 #else if $method.method == "pp.recipe_weinreb17"
36 sc.pp.recipe_weinreb17( 46 sc.pp.recipe_weinreb17(
37 adata=adata, 47 adata=adata,
38 log=$method.log, 48 log=$method.log,
39 mean_threshold=$method.mean_threshold, 49 mean_threshold=$method.mean_threshold,
40 cv_threshold=$method.cv_threshold, 50 cv_threshold=$method.cv_threshold,
41 n_pcs=$method.n_pcs, 51 n_pcs=$method.n_pcs,
42 svd_solver='$method.svd_solver', 52 svd_solver='$method.svd_solver',
43 random_state=$method.random_state, 53 random_state=$method.random_state,
44 copy=False) 54 copy=False)
45 #elif $method.method == "pp.recipe_seurat" 55
56 #else if $method.method == "pp.recipe_seurat"
46 sc.pp.recipe_seurat( 57 sc.pp.recipe_seurat(
47 adata=adata, 58 adata=adata,
48 log=$method.log, 59 log=$method.log,
49 plot=False, 60 plot=False,
50 copy=False) 61 copy=False)
51 #elif $method.method == "pp.log1p" 62
52 sc.pp.log1p(
53 data=adata,
54 copy=False)
55 #elif $method.method == "pp.scale"
56 sc.pp.scale(
57 data=adata,
58 zero_center=$method.zero_center,
59 #if $method.max_value
60 max_value=$method.max_value,
61 #end if
62 copy=False)
63 #elif $method.method == "pp.sqrt"
64 sc.pp.sqrt(
65 data=adata,
66 copy=False)
67 #elif $method.method == "pp.downsample_counts"
68 sc.pp.downsample_counts(
69 adata=adata,
70 target_counts=$method.target_counts,
71 random_state=$method.random_state,
72 copy=False)
73 #end if 63 #end if
74 64
75 @CMD_anndata_write_outputs@ 65 @CMD_anndata_write_outputs@
76 66
77 ]]></configfile> 67 ]]></configfile>
78 </configfiles> 68 </configfiles>
79 <inputs> 69 <inputs>
80 <expand macro="inputs_anndata"/> 70 <expand macro="inputs_anndata"/>
81 <conditional name="method"> 71 <conditional name="method">
82 <param argument="method" type="select" label="Method used for plotting"> 72 <param argument="method" type="select" label="Method used for normalization">
83 <option value="pp.normalize_per_cell">Normalize total counts per cell, using `pp.normalize_per_cell`</option> 73 <option value="pp.normalize_total">Normalize counts per cell, using `pp.normalize_total`</option>
84 <option value="pp.recipe_zheng17">Normalization and filtering as of Zheng et al. (2017), using `pp.recipe_zheng17`</option> 74 <option value="pp.recipe_zheng17">Normalization and filtering as of Zheng et al. (2017), using `pp.recipe_zheng17`</option>
85 <option value="pp.recipe_weinreb17">Normalization and filtering as of Weinreb et al (2017), using `pp.recipe_weinreb17`</option> 75 <option value="pp.recipe_weinreb17">Normalization and filtering as of Weinreb et al (2017), using `pp.recipe_weinreb17`</option>
86 <option value="pp.recipe_seurat">Normalization and filtering as of Seurat et al (2015), using `pp.recipe_seurat`</option> 76 <option value="pp.recipe_seurat">Normalization and filtering as of Seurat et al (2015), using `pp.recipe_seurat`</option>
87 <option value="pp.log1p">Logarithmize the data matrix, using `pp.log1p`</option>
88 <option value="pp.scale">Scale data to unit variance and zero mean, using `pp.scale`</option>
89 <option value="pp.sqrt">Square root the data matrix, using `pp.sqrt`</option>
90 <option value="pp.downsample_counts">Downsample counts, using `pp.downsample_counts`</option>
91 </param> 77 </param>
92 <when value="pp.normalize_per_cell"> 78 <when value="pp.normalize_total">
93 <param argument="counts_per_cell_after" type="float" value="" optional="true" label="Counts per cell after" help="If not provided, after normalization, each cell has a total count equal to the median of the *counts_per_cell* before normalization."/> 79 <param argument="target_sum" type="float" value="" optional="true" label="Target sum" help="If not provided, after normalization, each observation (cell) has a total count equal to the median of the total counts (cells) before normalization."/>
94 <param argument="counts_per_cell" type="data" format="tabular,txt" optional="true" label="Precomputed counts per cell" help=""/> 80 <conditional name="exclude_highly_expressed">
95 <param argument="key_n_counts" type="text" value="n_counts" label="Name of the field in `adata.obs` where the total counts per cell will be stored" help=""/> 81 <param argument="exclude_highly_expressed" type="select" label="Exclude (very) highly expressed genes for the computation of the normalization factor (size factor) for each cell" help=" A gene is considered highly expressed, if it has more than max_fraction of the total counts in at least one cell. The not-excluded genes will sum up to target_sum">
82 <option value="True">Yes</option>
83 <option value="False" selected="true">No</option>
84 </param>
85 <when value="True">
86 <param argument="max_fraction" type="float" value="0.05" label="Target sum" help="If not provided, after normalization, each observation (cell) has a total count equal to the median of the total counts (cells) before normalization."/>
87 </when>
88 <when value="False"/>
89 </conditional>
90 <param argument="key_added" type="text" value="n_counts" label="Name of the field in `adata.obs` where the normalization factor is stored" help=""/>
91 <param argument="layers" type="text" value="all" label="List of layers to normalize" help="'All' will normalize all layers. The list should be comma-separated."/>
92 <param argument="layer_norm" type="select" label="How to normalize layers?">
93 <option value="None">None: after normalization, for each layer in layers each cell has a total count equal to the median of the median of the total counts (cells) before normalization of the layer.</option>
94 <option value="after">After: for each layer in layers each cell has a total count equal to target_sum.</option>
95 <option value="X">X: for each layer in layers each cell has a total count equal to the median of total counts for observations (cells) of adata.X before normalization.</option>
96 </param>
96 </when> 97 </when>
97 <when value="pp.recipe_zheng17"> 98 <when value="pp.recipe_zheng17">
98 <param argument="n_top_genes" type="integer" min="0" value="1000" label="Number of genes to keep" help=""/> 99 <param argument="n_top_genes" type="integer" min="0" value="1000" label="Number of genes to keep" help=""/>
99 <expand macro="param_log"/> 100 <expand macro="param_log"/>
100 </when> 101 </when>
107 <expand macro="pca_random_state"/> 108 <expand macro="pca_random_state"/>
108 </when> 109 </when>
109 <when value="pp.recipe_seurat"> 110 <when value="pp.recipe_seurat">
110 <expand macro="param_log"/> 111 <expand macro="param_log"/>
111 </when> 112 </when>
112 <when value="pp.log1p"/>
113 <when value="pp.scale">
114 <param argument="zero_center" type="boolean" truevalue="True" falsevalue="False" checked="true"
115 label="Zero center?" help="If not, it omits zero-centering variables, which allows to handle sparse input efficiently."/>
116 <param argument="max_value" type="float" value="" optional="true" label="Maximum value"
117 help="Clip (truncate) to this value after scaling. If not set, it does not clip."/>
118 </when>
119 <when value="pp.sqrt"/>
120 <when value="pp.downsample_counts">
121 <param argument="target_counts" type="integer" min="0" value="20000"
122 label="Target number of counts for downsampling" help="Cells with more counts than 'target_counts' will be downsampled to have 'target_counts' counts."/>
123 <param argument="random_state" type="integer" value="0" label="Random seed to change subsampling" help=""/>
124 </when>
125 </conditional> 113 </conditional>
126 <expand macro="anndata_output_format"/>
127 </inputs> 114 </inputs>
128 <outputs> 115 <outputs>
129 <expand macro="anndata_outputs"/> 116 <expand macro="anndata_outputs"/>
130 <data name="anndata_obs" format="tabular" label="${tool.name} on ${on_string}: Annotation of observations">
131 <filter>method['method'] == 'pp.normalize_per_cell'</filter>
132 </data>
133 </outputs> 117 </outputs>
134 <tests> 118 <tests>
135 <test> 119 <test>
136 <conditional name="input"> 120 <!-- test 1 -->
137 <param name="format" value="h5ad" /> 121 <param name="adata" value="krumsiek11.h5ad" />
138 <param name="adata" value="krumsiek11.h5ad" /> 122 <conditional name="method">
139 </conditional> 123 <param name="method" value="pp.normalize_total"/>
140 <conditional name="method"> 124 <conditional name="exclude_highly_expressed">
141 <param name="method" value="pp.normalize_per_cell"/> 125 <param name="exclude_highly_expressed" value="False"/>
142 <param name="counts_per_cell_after" value="2"/> 126 </conditional>
143 <param name="counts_per_cell" value="krumsiek11_counts_per_cell"/> 127 <param name="key_added" value="n_counts"/>
144 <param name="key_n_counts" value="n_counts"/> 128 <param name="layers" value="all"/>
145 </conditional> 129 <param name="layer_norm" value="None"/>
146 <param name="anndata_output_format" value="h5ad"/> 130 </conditional>
147 <assert_stdout> 131 <assert_stdout>
148 <has_text_matching expression="sc.pp.normalize_per_cell"/> 132 <has_text_matching expression="sc.pp.normalize_total"/>
149 <has_text_matching expression="counts_per_cell_after=2.0"/> 133 <has_text_matching expression="exclude_highly_expressed=False"/>
150 <has_text_matching expression="counts_per_cell=np.loadtxt"/> 134 <has_text_matching expression="key_added='n_counts'"/>
151 <has_text_matching expression="key_n_counts='n_counts'"/> 135 <has_text_matching expression="layers='all'"/>
152 </assert_stdout> 136 </assert_stdout>
153 <output name="anndata_out_h5ad" file="pp.normalize_per_cell.krumsiek11.h5ad" ftype="h5" compare="sim_size"/> 137 <output name="anndata_out" file="pp.normalize_total.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
154 <output name="anndata_obs" file="pp.normalize_per_cell.obs.krumsiek11.tabular"/> 138 </test>
155 </test> 139 <test>
156 <test> 140 <!-- test 2 -->
157 <conditional name="input"> 141 <param name="adata" value="random-randint.h5ad"/>
158 <param name="format" value="h5ad" />
159 <param name="adata" value="random-randint.h5ad"/>
160 </conditional>
161 <conditional name="method"> 142 <conditional name="method">
162 <param name="method" value="pp.recipe_zheng17"/> 143 <param name="method" value="pp.recipe_zheng17"/>
163 <param name="n_top_genes" value="1000"/> 144 <param name="n_top_genes" value="1000"/>
164 <param name="log" value="True"/> 145 <param name="log" value="True"/>
165 </conditional> 146 </conditional>
166 <param name="anndata_output_format" value="h5ad"/>
167 <assert_stdout> 147 <assert_stdout>
168 <has_text_matching expression="sc.pp.recipe_zheng17"/> 148 <has_text_matching expression="sc.pp.recipe_zheng17"/>
169 <has_text_matching expression="n_top_genes=1000"/> 149 <has_text_matching expression="n_top_genes=1000"/>
170 <has_text_matching expression="log=True"/> 150 <has_text_matching expression="log=True"/>
171 </assert_stdout> 151 </assert_stdout>
172 <output name="anndata_out_h5ad" file="pp.recipe_zheng17.random-randint.h5ad" ftype="h5" compare="sim_size"/> 152 <output name="anndata_out" file="pp.recipe_zheng17.random-randint.h5ad" ftype="h5ad" compare="sim_size"/>
173 </test> 153 </test>
174 <test> 154 <test>
175 <conditional name="input"> 155 <!-- test 3 -->
176 <param name="format" value="h5ad" /> 156 <param name="adata" value="paul15_subsample.h5ad" />
177 <param name="adata" value="paul15_subsample.h5ad" />
178 </conditional>
179 <conditional name="method"> 157 <conditional name="method">
180 <param name="method" value="pp.recipe_weinreb17"/> 158 <param name="method" value="pp.recipe_weinreb17"/>
181 <param name="log" value="True"/> 159 <param name="log" value="True"/>
182 <param name="mean_threshold" value="0.01"/> 160 <param name="mean_threshold" value="0.01"/>
183 <param name="cv_threshold" value="2.0"/> 161 <param name="cv_threshold" value="2.0"/>
184 <param name="n_pcs" value="50"/> 162 <param name="n_pcs" value="50"/>
185 <param name="svd_solver" value="randomized"/> 163 <param name="svd_solver" value="randomized"/>
186 <param name="random_state" value="0"/> 164 <param name="random_state" value="0"/>
187 </conditional> 165 </conditional>
188 <param name="anndata_output_format" value="h5ad" />
189 <assert_stdout> 166 <assert_stdout>
190 <has_text_matching expression="sc.pp.recipe_weinreb17"/> 167 <has_text_matching expression="sc.pp.recipe_weinreb17"/>
191 <has_text_matching expression="log=True"/> 168 <has_text_matching expression="log=True"/>
192 <has_text_matching expression="mean_threshold=0.01"/> 169 <has_text_matching expression="mean_threshold=0.01"/>
193 <has_text_matching expression="cv_threshold=2.0"/> 170 <has_text_matching expression="cv_threshold=2.0"/>
194 <has_text_matching expression="n_pcs=50"/> 171 <has_text_matching expression="n_pcs=50"/>
195 <has_text_matching expression="svd_solver='randomized'"/> 172 <has_text_matching expression="svd_solver='randomized'"/>
196 <has_text_matching expression="random_state=0"/> 173 <has_text_matching expression="random_state=0"/>
197 </assert_stdout> 174 </assert_stdout>
198 <output name="anndata_out_h5ad" file="pp.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5" compare="sim_size"/> 175 <output name="anndata_out" file="pp.recipe_weinreb17.paul15_subsample.updated.h5ad" ftype="h5ad" compare="sim_size"/>
199 </test> 176 </test>
200 <test> 177 <test>
201 <conditional name="input"> 178 <!-- test 4 -->
202 <param name="format" value="h5ad" /> 179 <param name="adata" value="pp.recipe_zheng17.random-randint.h5ad" />
203 <param name="adata" value="pp.recipe_zheng17.random-randint.h5ad" />
204 </conditional>
205 <conditional name="method"> 180 <conditional name="method">
206 <param name="method" value="pp.recipe_seurat"/> 181 <param name="method" value="pp.recipe_seurat"/>
207 <param name="log" value="True"/> 182 <param name="log" value="True"/>
208 </conditional> 183 </conditional>
209 <param name="anndata_output_format" value="h5ad"/>
210 <assert_stdout> 184 <assert_stdout>
211 <has_text_matching expression="sc.pp.recipe_seurat"/> 185 <has_text_matching expression="sc.pp.recipe_seurat"/>
212 <has_text_matching expression="log=True"/> 186 <has_text_matching expression="log=True"/>
213 </assert_stdout> 187 </assert_stdout>
214 <output name="anndata_out_h5ad" file="pp.recipe_seurat.recipe_zheng17.h5ad" ftype="h5" compare="sim_size"/> 188 <output name="anndata_out" file="pp.recipe_seurat.recipe_zheng17.h5ad" ftype="h5ad" compare="sim_size"/>
215 </test> 189 </test>
216 <test> 190
217 <conditional name="input">
218 <param name="format" value="h5ad" />
219 <param name="adata" value="krumsiek11.h5ad" />
220 </conditional>
221 <conditional name="method">
222 <param name="method" value="pp.log1p"/>
223 </conditional>
224 <param name="anndata_output_format" value="h5ad" />
225 <assert_stdout>
226 <has_text_matching expression="sc.pp.log1p"/>
227 </assert_stdout>
228 <output name="anndata_out_h5ad" file="pp.log1p.krumsiek11.h5ad" ftype="h5" compare="sim_size"/>
229 </test>
230 <test>
231 <conditional name="input">
232 <param name="format" value="h5ad" />
233 <param name="adata" value="krumsiek11.h5ad" />
234 </conditional>
235 <conditional name="method">
236 <param name="method" value="pp.scale"/>
237 <param name="zero_center" value="true"/>
238 </conditional>
239 <param name="anndata_output_format" value="h5ad" />
240 <assert_stdout>
241 <has_text_matching expression="sc.pp.scale"/>
242 <has_text_matching expression="zero_center=True"/>
243 </assert_stdout>
244 <output name="anndata_out_h5ad" file="pp.scale.krumsiek11.h5ad" ftype="h5" compare="sim_size"/>
245 </test>
246 <test>
247 <conditional name="input">
248 <param name="format" value="h5ad" />
249 <param name="adata" value="krumsiek11.h5ad" />
250 </conditional>
251 <conditional name="method">
252 <param name="method" value="pp.scale"/>
253 <param name="zero_center" value="true"/>
254 <param name="max_value" value="10"/>
255 </conditional>
256 <param name="anndata_output_format" value="h5ad" />
257 <assert_stdout>
258 <has_text_matching expression="sc.pp.scale"/>
259 <has_text_matching expression="zero_center=True"/>
260 <has_text_matching expression="max_value=10.0"/>
261 </assert_stdout>
262 <output name="anndata_out_h5ad" file="pp.scale_max_value.krumsiek11.h5ad" ftype="h5" compare="sim_size"/>
263 </test>
264 <test>
265 <conditional name="input">
266 <param name="format" value="h5ad" />
267 <param name="adata" value="krumsiek11.h5ad" />
268 </conditional>
269 <conditional name="method">
270 <param name="method" value="pp.sqrt"/>
271 </conditional>
272 <param name="anndata_output_format" value="h5ad" />
273 <assert_stdout>
274 <has_text_matching expression="sc.pp.sqrt"/>
275 </assert_stdout>
276 <output name="anndata_out_h5ad" file="pp.sqrt.krumsiek11.h5ad" ftype="h5" compare="sim_size"/>
277 </test>
278 <test>
279 <conditional name="input">
280 <param name="format" value="h5ad" />
281 <param name="adata" value="random-randint.h5ad" />
282 </conditional>
283 <conditional name="method">
284 <param name="method" value="pp.downsample_counts"/>
285 <param name="target_counts" value="20000"/>
286 <param name="random_state" value="0"/>
287 </conditional>
288 <param name="anndata_output_format" value="h5ad" />
289 <assert_stdout>
290 <has_text_matching expression="sc.pp.downsample_counts"/>
291 <has_text_matching expression="target_counts=20000"/>
292 <has_text_matching expression="random_state=0"/>
293 </assert_stdout>
294 <output name="anndata_out_h5ad" ftype="h5">
295 <assert_contents>
296 <has_h5_keys keys="X, obs, var" />
297 </assert_contents>
298 </output>
299 </test>
300 </tests> 191 </tests>
301 <help><![CDATA[ 192 <help><![CDATA[
302 Normalize total counts per cell (`pp.normalize_per_cell`) 193 Normalize total counts per cell (`pp.normalize_per_cell`)
303 ========================================================= 194 =========================================================
304 195
306 the same total count after normalization. 197 the same total count after normalization.
307 198
308 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING. 199 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING.
309 200
310 More details on the `scanpy documentation 201 More details on the `scanpy documentation
311 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pp.normalize_per_cell.html>`__ 202 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.normalize_per_cell.html>`__
312 203
313 204
314 Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`) 205 Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`)
315 ================================================================================================================== 206 ==================================================================================================================
316 207
325 - renormalize after filtering 216 - renormalize after filtering
326 - log transform (if needed) 217 - log transform (if needed)
327 - scale to unit variance and shift to zero mean 218 - scale to unit variance and shift to zero mean
328 219
329 More details on the `scanpy documentation 220 More details on the `scanpy documentation
330 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pp.recipe_zheng17.html>`__ 221 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_zheng17.html>`__
331 222
332 223
333 Normalization and filtering as of Weinreb et al (2017) (`pp.recipe_weinreb17`) 224 Normalization and filtering as of Weinreb et al (2017) (`pp.recipe_weinreb17`)
334 ============================================================================== 225 ==============================================================================
335 226
336 Expects non-logarithmized data. If using logarithmized data, pass `log=False`. 227 Expects non-logarithmized data. If using logarithmized data, pass `log=False`.
337 228
338 More details on the `scanpy documentation 229 More details on the `scanpy documentation
339 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pp.recipe_weinreb17.html>`__ 230 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_weinreb17.html>`__
340 231
341 232
342 Normalization and filtering as of Seurat et al (2015) (`pp.recipe_seurat`) 233 Normalization and filtering as of Seurat et al (2015) (`pp.recipe_seurat`)
343 ========================================================================== 234 ==========================================================================
344 235
345 This uses a particular preprocessing. 236 This uses a particular preprocessing.
346 237
347 Expects non-logarithmized data. If using logarithmized data, pass `log=False`. 238 Expects non-logarithmized data. If using logarithmized data, pass `log=False`.
348 239
349 More details on the `scanpy documentation 240 More details on the `scanpy documentation
350 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pp.recipe_seurat.html>`__ 241 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_seurat.html>`__
351
352 Logarithmize the data matrix (`pp.log1p`)
353 =========================================
354
355 More details on the `scanpy documentation
356 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pp.log1p.html>`__
357
358 Scale data to unit variance and zero mean (`pp.scale`)
359 ======================================================
360
361 More details on the `scanpy documentation
362 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pp.scale.html>`__
363
364 Computes the square root the data matrix (`pp.sqrt`)
365 ====================================================
366
367 `X = sqrt(X)`
368
369 Downsample counts (`pp.downsample_counts`)
370 ==========================================
371
372 Downsample counts so that each cell has no more than `target_counts`. Cells with fewer counts than `target_counts` are unaffected by this. This
373 has been implemented by M. D. Luecken.
374
375 More details on the `scanpy documentation
376 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pp.downsample_counts.html>`__
377 242
378 ]]></help> 243 ]]></help>
379 <expand macro="citations"/> 244 <expand macro="citations"/>
380 </tool> 245 </tool>