Mercurial > repos > iuc > scanpy_plot

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
author iuc
date Sat, 18 May 2024 18:32:22 +0000
parents 9b0cdb8cf6be
children
comparison
equal deleted inserted replaced
13:6f5349dd5c49 14:f7446fd8d5e7
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>