Mercurial > repos > iuc > scanpy_plot
comparison plot.xml @ 14:f7446fd8d5e7 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
author | iuc |
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date | Sat, 18 May 2024 18:32:22 +0000 |
parents | 9b0cdb8cf6be |
children |
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13:6f5349dd5c49 | 14:f7446fd8d5e7 |
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2297 | 2297 |
2298 If groupby is not given, the matrixplot assumes that all data belongs to a single | 2298 If groupby is not given, the matrixplot assumes that all data belongs to a single |
2299 category. | 2299 category. |
2300 | 2300 |
2301 More details on the `scanpy documentation | 2301 More details on the `scanpy documentation |
2302 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.matrixplot.html>`__ | 2302 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.matrixplot.html>`__ |
2303 | 2303 |
2304 Generic: Hierarchically-clustered heatmap (`pl.clustermap`) | 2304 Generic: Hierarchically-clustered heatmap (`pl.clustermap`) |
2305 =========================================================== | 2305 =========================================================== |
2306 | 2306 |
2307 Wraps `seaborn.clustermap | 2307 Wraps `seaborn.clustermap |
2315 clustergrid.dendrogram_row.reordered_ind | 2315 clustergrid.dendrogram_row.reordered_ind |
2316 | 2316 |
2317 Column indices, use: clustergrid.dendrogram_col.reordered_ind | 2317 Column indices, use: clustergrid.dendrogram_col.reordered_ind |
2318 | 2318 |
2319 More details on the `scanpy documentation | 2319 More details on the `scanpy documentation |
2320 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.clustermap.html>`__ | 2320 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.clustermap.html>`__ |
2321 | 2321 |
2322 Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`) | 2322 Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`) |
2323 ========================================================================================================= | 2323 ========================================================================================================= |
2324 | 2324 |
2325 Computes, for each gene, the fraction of counts assigned to that gene within | 2325 Computes, for each gene, the fraction of counts assigned to that gene within |
2327 plotted as boxplots. | 2327 plotted as boxplots. |
2328 | 2328 |
2329 This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")` | 2329 This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")` |
2330 | 2330 |
2331 More details on the `scanpy documentation | 2331 More details on the `scanpy documentation |
2332 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.highest_expr_genes.html>`__ | 2332 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.highest_expr_genes.html>`__ |
2333 | 2333 |
2334 Preprocessing: Plot dispersions versus means for genes (`pl.highly_variable_genes`) | 2334 Preprocessing: Plot dispersions versus means for genes (`pl.highly_variable_genes`) |
2335 =================================================================================== | 2335 =================================================================================== |
2336 | 2336 |
2337 It produces Supp. Fig. 5c of Zheng et al. (2017) and MeanVarPlot() of Seurat. | 2337 It produces Supp. Fig. 5c of Zheng et al. (2017) and MeanVarPlot() of Seurat. |
2338 | 2338 |
2339 More details on the `scanpy documentation | 2339 More details on the `scanpy documentation |
2340 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.highly_variable_genes.html>`__ | 2340 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.highly_variable_genes.html>`__ |
2341 | 2341 |
2342 PCA: Scatter plot in PCA coordinates (`pl.pca`) | 2342 PCA: Scatter plot in PCA coordinates (`pl.pca`) |
2343 =============================================== | 2343 =============================================== |
2344 | 2344 |
2345 More details on the `scanpy documentation | 2345 More details on the `scanpy documentation |
2346 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca.html>`__ | 2346 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca.html>`__ |
2347 | 2347 |
2348 PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`) | 2348 PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`) |
2349 ===================================================================== | 2349 ===================================================================== |
2350 | 2350 |
2351 More details on the `scanpy documentation | 2351 More details on the `scanpy documentation |
2352 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_loadings.html>`__ | 2352 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_loadings.html>`__ |
2353 | 2353 |
2354 PCA: Plot the variance ratio (`pl.pca_variance_ratio`) | 2354 PCA: Plot the variance ratio (`pl.pca_variance_ratio`) |
2355 ====================================================== | 2355 ====================================================== |
2356 | 2356 |
2357 More details on the `scanpy documentation | 2357 More details on the `scanpy documentation |
2358 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_variance_ratio.html>`__ | 2358 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_variance_ratio.html>`__ |
2359 | 2359 |
2360 PCA: Plot PCA results (`pl.pca_overview`) | 2360 PCA: Plot PCA results (`pl.pca_overview`) |
2361 ========================================= | 2361 ========================================= |
2362 | 2362 |
2363 The parameters are the ones of the scatter plot. Call pca_ranking separately | 2363 The parameters are the ones of the scatter plot. Call pca_ranking separately |
2364 if you want to change the default settings. | 2364 if you want to change the default settings. |
2365 | 2365 |
2366 More details on the `scanpy documentation | 2366 More details on the `scanpy documentation |
2367 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_overview.html>`__ | 2367 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_overview.html>`__ |
2368 | 2368 |
2369 Embedding: Scatter plot in tSNE basis (`pl.tsne`) | 2369 Embedding: Scatter plot in tSNE basis (`pl.tsne`) |
2370 ================================================= | 2370 ================================================= |
2371 | 2371 |
2372 More details on the `scanpy documentation | 2372 More details on the `scanpy documentation |
2373 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.tsne.html>`__ | 2373 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.tsne.html>`__ |
2374 | 2374 |
2375 Embeddings: Scatter plot in UMAP basis (`pl.umap`) | 2375 Embeddings: Scatter plot in UMAP basis (`pl.umap`) |
2376 ================================================== | 2376 ================================================== |
2377 | 2377 |
2378 More details on the `scanpy documentation | 2378 More details on the `scanpy documentation |
2379 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.umap.html>`__ | 2379 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.umap.html>`__ |
2380 | 2380 |
2381 Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`) | 2381 Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`) |
2382 ============================================================== | 2382 ============================================================== |
2383 | 2383 |
2384 More details on the `scanpy documentation | 2384 More details on the `scanpy documentation |
2385 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.diffmap.html>`__ | 2385 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.diffmap.html>`__ |
2386 | 2386 |
2387 Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`) | 2387 Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`) |
2388 =========================================================================================================== | 2388 =========================================================================================================== |
2389 | 2389 |
2390 More details on the `scanpy documentation | 2390 More details on the `scanpy documentation |
2391 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.dpt_groups_pseudotime.html>`__ | 2391 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_groups_pseudotime.html>`__ |
2392 | 2392 |
2393 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`) | 2393 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`) |
2394 ===================================================================================================== | 2394 ===================================================================================================== |
2395 | 2395 |
2396 More details on the `scanpy documentation | 2396 More details on the `scanpy documentation |
2397 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.dpt_timeseries.html>`__ | 2397 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_timeseries.html>`__ |
2398 | 2398 |
2399 | 2399 |
2400 Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`) | 2400 Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`) |
2401 ==================================================================================================================================== | 2401 ==================================================================================================================================== |
2402 | 2402 |
2405 When initializing the positions, note that - for some reason - igraph | 2405 When initializing the positions, note that - for some reason - igraph |
2406 mirrors coordinates along the x axis... that is, you should increase the | 2406 mirrors coordinates along the x axis... that is, you should increase the |
2407 `maxiter` parameter by 1 if the layout is flipped. | 2407 `maxiter` parameter by 1 if the layout is flipped. |
2408 | 2408 |
2409 More details on the `scanpy documentation | 2409 More details on the `scanpy documentation |
2410 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga.html>`__ | 2410 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga.html>`__ |
2411 | 2411 |
2412 | 2412 |
2413 Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side (`pl.paga_compare`) | 2413 Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side (`pl.paga_compare`) |
2414 ========================================================================================================== | 2414 ========================================================================================================== |
2415 | 2415 |
2416 More details on the `scanpy documentation | 2416 More details on the `scanpy documentation |
2417 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga_compare.html>`__ | 2417 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga_compare.html>`__ |
2418 | 2418 |
2419 Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths (`pl.paga_path`) | 2419 Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths (`pl.paga_path`) |
2420 ====================================================================================================================== | 2420 ====================================================================================================================== |
2421 | 2421 |
2422 More details on the `scanpy documentation | 2422 More details on the `scanpy documentation |
2423 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga_path.html>`__ | 2423 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga_path.html>`__ |
2424 | 2424 |
2425 Marker genes: Plot ranking of genes using dotplot plot (`pl.rank_genes_groups`) | 2425 Marker genes: Plot ranking of genes using dotplot plot (`pl.rank_genes_groups`) |
2426 =============================================================================== | 2426 =============================================================================== |
2427 | 2427 |
2428 More details on the `scanpy documentation | 2428 More details on the `scanpy documentation |
2429 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups.html>`__ | 2429 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups.html>`__ |
2430 | 2430 |
2431 Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`) | 2431 Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`) |
2432 ================================================================================== | 2432 ================================================================================== |
2433 | 2433 |
2434 More details on the `scanpy documentation | 2434 More details on the `scanpy documentation |
2435 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_violin.html>`__ | 2435 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_violin.html>`__ |
2436 | 2436 |
2437 Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`) | 2437 Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`) |
2438 ==================================================================================== | 2438 ==================================================================================== |
2439 | 2439 |
2440 More details on the `scanpy documentation | 2440 More details on the `scanpy documentation |
2441 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_dotplot.html>`__ | 2441 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_dotplot.html>`__ |
2442 | 2442 |
2443 Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`) | 2443 Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`) |
2444 ==================================================================================== | 2444 ==================================================================================== |
2445 | 2445 |
2446 More details on the `scanpy documentation | 2446 More details on the `scanpy documentation |
2447 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_heatmap.html>`__ | 2447 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_heatmap.html>`__ |
2448 | 2448 |
2449 Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`) | 2449 Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`) |
2450 ========================================================================================== | 2450 ========================================================================================== |
2451 | 2451 |
2452 More details on the `scanpy documentation | 2452 More details on the `scanpy documentation |
2453 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_matrixplot.html>`__ | 2453 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_matrixplot.html>`__ |
2454 | 2454 |
2455 Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`) | 2455 Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`) |
2456 ================================================================================================== | 2456 ================================================================================================== |
2457 | 2457 |
2458 More details on the `scanpy documentation | 2458 More details on the `scanpy documentation |
2459 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__ | 2459 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_stacked_violin.html>`__ |
2460 ]]></help> | 2460 ]]></help> |
2461 <expand macro="citations"/> | 2461 <expand macro="citations"/> |
2462 </tool> | 2462 </tool> |