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comparison plot.xml @ 1:fee4b4eb0ef5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
author iuc
date Tue, 05 Nov 2024 11:55:07 +0000
parents 2622dd85416f
children
comparison
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0:2622dd85416f 1:fee4b4eb0ef5
1 <tool id="seurat_plot" name="Seurat Visualize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="seurat_plot" name="Seurat Visualize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>- Plot cells, features and dimensions</description> 2 <description>- Plot cells, features and dimensions</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 @CMD@ 10 @CMD@
10 ]]></command> 11 ]]></command>
1175 <https://satijalab.org/seurat/reference/vlnplot>`__ 1176 <https://satijalab.org/seurat/reference/vlnplot>`__
1176 1177
1177 FeatureScatter 1178 FeatureScatter
1178 ============== 1179 ==============
1179 1180
1180 Create a scatter plot of two features (typically feature expression), across a set of single cells. Cells are colored by their identity class. 1181 Create a scatter plot of two features (typically feature expression), across a set of single cells. Cells are colored by their identity class.
1181 Pearson correlation between the two features is displayed above the plot. 1182 Pearson correlation between the two features is displayed above the plot.
1182 1183
1183 More details on the `seurat documentation 1184 More details on the `seurat documentation
1184 <https://satijalab.org/seurat/reference/featurescatter>`__ 1185 <https://satijalab.org/seurat/reference/featurescatter>`__
1185 1186
1208 <https://satijalab.org/seurat/reference/vizdimloadings>`__ 1209 <https://satijalab.org/seurat/reference/vizdimloadings>`__
1209 1210
1210 DimPlot 1211 DimPlot
1211 ======= 1212 =======
1212 1213
1213 Graph the output of a dimensional reduction technique on a 2D scatter plot where each point is a cell and it's positioned based on the cell embeddings determined by the reduction technique. 1214 Graph the output of a dimensional reduction technique on a 2D scatter plot where each point is a cell and it's positioned based on the cell embeddings determined by the reduction technique.
1214 By default, cells are colored by their identity class (can be changed with the group.by parameter). 1215 By default, cells are colored by their identity class (can be changed with the group.by parameter).
1215 1216
1216 More details on the `seurat documentation 1217 More details on the `seurat documentation
1217 <https://satijalab.org/seurat/reference/dimplot>`__ 1218 <https://satijalab.org/seurat/reference/dimplot>`__
1218 1219
1219 DimHeatmap 1220 DimHeatmap
1220 ========== 1221 ==========
1221 1222
1222 Draw a heatmap focusing on a principal component. Both cells and genes are sorted by their principal component scores. 1223 Draw a heatmap focusing on a principal component. Both cells and genes are sorted by their principal component scores.
1223 Allows for nice visualization of sources of heterogeneity in the dataset. 1224 Allows for nice visualization of sources of heterogeneity in the dataset.
1224 1225
1225 More details on the `seurat documentation 1226 More details on the `seurat documentation
1226 <https://satijalab.org/seurat/reference/dimheatmap>`__ 1227 <https://satijalab.org/seurat/reference/dimheatmap>`__
1227 1228
1228 ElbowPlot 1229 ElbowPlot
1229 ========= 1230 =========
1230 1231
1231 Plot the standard deviations of the principal components for easy identification of an elbow in the graph - plots PCA as default reduction. 1232 Plot the standard deviations of the principal components for easy identification of an elbow in the graph - plots PCA as default reduction.
1232 1233
1233 More details on the `seurat documentation 1234 More details on the `seurat documentation
1234 <https://satijalab.org/seurat/reference/elbowplot>`__ 1235 <https://satijalab.org/seurat/reference/elbowplot>`__
1235 1236
1236 FeaturePlot 1237 FeaturePlot
1250 <https://satijalab.org/seurat/reference/doheatmap>`__ 1251 <https://satijalab.org/seurat/reference/doheatmap>`__
1251 1252
1252 DotPlot 1253 DotPlot
1253 ======= 1254 =======
1254 1255
1255 Visualize how feature expression changes across different identity classes (e.g. clusters). 1256 Visualize how feature expression changes across different identity classes (e.g. clusters).
1256 The size of the dot encodes the percentage of cells within a class that express the gene, while the color encodes the AverageExpression level across all cells within a class. 1257 The size of the dot encodes the percentage of cells within a class that express the gene, while the color encodes the AverageExpression level across all cells within a class.
1257 1258
1258 More details on the `seurat documentation 1259 More details on the `seurat documentation
1259 <https://satijalab.org/seurat/reference/dotplot>`__ 1260 <https://satijalab.org/seurat/reference/dotplot>`__
1260 1261