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comparison plot.xml @ 5:f2323ff4e07f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
author iuc
date Mon, 10 Feb 2020 10:16:27 +0000
parents 22c1b4b70360
children 7c8b155300d4
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4:f05870ae0bab 5:f2323ff4e07f
1776 1776
1777 If groupby is not given, the matrixplot assumes that all data belongs to a single 1777 If groupby is not given, the matrixplot assumes that all data belongs to a single
1778 category. 1778 category.
1779 1779
1780 More details on the `scanpy documentation 1780 More details on the `scanpy documentation
1781 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.matrixplot.html>`__ 1781 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.matrixplot.html>`__
1782 1782
1783 Generic: Hierarchically-clustered heatmap (`pl.clustermap`) 1783 Generic: Hierarchically-clustered heatmap (`pl.clustermap`)
1784 =========================================================== 1784 ===========================================================
1785 1785
1786 Wraps `seaborn.clustermap 1786 Wraps `seaborn.clustermap
1794 clustergrid.dendrogram_row.reordered_ind 1794 clustergrid.dendrogram_row.reordered_ind
1795 1795
1796 Column indices, use: clustergrid.dendrogram_col.reordered_ind 1796 Column indices, use: clustergrid.dendrogram_col.reordered_ind
1797 1797
1798 More details on the `scanpy documentation 1798 More details on the `scanpy documentation
1799 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.clustermap.html>`__ 1799 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.clustermap.html>`__
1800 1800
1801 Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`) 1801 Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`)
1802 ========================================================================================================= 1802 =========================================================================================================
1803 1803
1804 Computes, for each gene, the fraction of counts assigned to that gene within 1804 Computes, for each gene, the fraction of counts assigned to that gene within
1806 plotted as boxplots. 1806 plotted as boxplots.
1807 1807
1808 This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")` 1808 This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")`
1809 1809
1810 More details on the `scanpy documentation 1810 More details on the `scanpy documentation
1811 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.highest_expr_genes.html>`__ 1811 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.highest_expr_genes.html>`__
1812 1812
1813 Preprocessing: Plot dispersions versus means for genes (`pl.highly_variable_genes`) 1813 Preprocessing: Plot dispersions versus means for genes (`pl.highly_variable_genes`)
1814 =================================================================================== 1814 ===================================================================================
1815 1815
1816 It produces Supp. Fig. 5c of Zheng et al. (2017) and MeanVarPlot() of Seurat. 1816 It produces Supp. Fig. 5c of Zheng et al. (2017) and MeanVarPlot() of Seurat.
1817 1817
1818 More details on the `scanpy documentation 1818 More details on the `scanpy documentation
1819 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.highly_variable_genes.html>`__ 1819 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.highly_variable_genes.html>`__
1820 1820
1821 PCA: Scatter plot in PCA coordinates (`pl.pca`) 1821 PCA: Scatter plot in PCA coordinates (`pl.pca`)
1822 =============================================== 1822 ===============================================
1823 1823
1824 More details on the `scanpy documentation 1824 More details on the `scanpy documentation
1825 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca.html>`__ 1825 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.pca.html>`__
1826 1826
1827 PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`) 1827 PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`)
1828 ===================================================================== 1828 =====================================================================
1829 1829
1830 More details on the `scanpy documentation 1830 More details on the `scanpy documentation
1831 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_loadings.html>`__ 1831 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.pca_loadings.html>`__
1832 1832
1833 PCA: Plot the variance ratio (`pl.pca_variance_ratio`) 1833 PCA: Plot the variance ratio (`pl.pca_variance_ratio`)
1834 ====================================================== 1834 ======================================================
1835 1835
1836 More details on the `scanpy documentation 1836 More details on the `scanpy documentation
1837 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_variance_ratio.html>`__ 1837 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.pca_variance_ratio.html>`__
1838 1838
1839 PCA: Plot PCA results (`pl.pca_overview`) 1839 PCA: Plot PCA results (`pl.pca_overview`)
1840 ========================================= 1840 =========================================
1841 1841
1842 The parameters are the ones of the scatter plot. Call pca_ranking separately 1842 The parameters are the ones of the scatter plot. Call pca_ranking separately
1843 if you want to change the default settings. 1843 if you want to change the default settings.
1844 1844
1845 More details on the `scanpy documentation 1845 More details on the `scanpy documentation
1846 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_overview.html>`__ 1846 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.pca_overview.html>`__
1847 1847
1848 Embedding: Scatter plot in tSNE basis (`pl.tsne`) 1848 Embedding: Scatter plot in tSNE basis (`pl.tsne`)
1849 ================================================= 1849 =================================================
1850 1850
1851 More details on the `scanpy documentation 1851 More details on the `scanpy documentation
1852 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.tsne.html>`__ 1852 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.tsne.html>`__
1853 1853
1854 Embeddings: Scatter plot in UMAP basis (`pl.umap`) 1854 Embeddings: Scatter plot in UMAP basis (`pl.umap`)
1855 ================================================== 1855 ==================================================
1856 1856
1857 More details on the `scanpy documentation 1857 More details on the `scanpy documentation
1858 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.umap.html>`__ 1858 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.umap.html>`__
1859 1859
1860 Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`) 1860 Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`)
1861 ============================================================== 1861 ==============================================================
1862 1862
1863 More details on the `scanpy documentation 1863 More details on the `scanpy documentation
1864 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.diffmap.html>`__ 1864 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.diffmap.html>`__
1865 1865
1866 Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`) 1866 Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)
1867 =========================================================================================================== 1867 ===========================================================================================================
1868 1868
1869 More details on the `scanpy documentation 1869 More details on the `scanpy documentation
1870 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.dpt_groups_pseudotime.html>`__ 1870 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.dpt_groups_pseudotime.html>`__
1871 1871
1872 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`) 1872 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`)
1873 ===================================================================================================== 1873 =====================================================================================================
1874 1874
1875 More details on the `scanpy documentation 1875 More details on the `scanpy documentation
1876 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.dpt_timeseries.html>`__ 1876 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.dpt_timeseries.html>`__
1877 1877
1878 1878
1879 Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`) 1879 Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`)
1880 ==================================================================================================================================== 1880 ====================================================================================================================================
1881 1881
1884 When initializing the positions, note that - for some reason - igraph 1884 When initializing the positions, note that - for some reason - igraph
1885 mirrors coordinates along the x axis... that is, you should increase the 1885 mirrors coordinates along the x axis... that is, you should increase the
1886 `maxiter` parameter by 1 if the layout is flipped. 1886 `maxiter` parameter by 1 if the layout is flipped.
1887 1887
1888 More details on the `scanpy documentation 1888 More details on the `scanpy documentation
1889 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga.html>`__ 1889 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.paga.html>`__
1890 1890
1891 1891
1892 Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side (`pl.paga_compare`) 1892 Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side (`pl.paga_compare`)
1893 ========================================================================================================== 1893 ==========================================================================================================
1894 1894
1895 More details on the `scanpy documentation 1895 More details on the `scanpy documentation
1896 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga_compare.html>`__ 1896 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.paga_compare.html>`__
1897 1897
1898 Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths (`pl.paga_path`) 1898 Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths (`pl.paga_path`)
1899 ====================================================================================================================== 1899 ======================================================================================================================
1900 1900
1901 More details on the `scanpy documentation 1901 More details on the `scanpy documentation
1902 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga_path.html>`__ 1902 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.paga_path.html>`__
1903 1903
1904 Marker genes: Plot ranking of genes using dotplot plot (`pl.rank_genes_groups`) 1904 Marker genes: Plot ranking of genes using dotplot plot (`pl.rank_genes_groups`)
1905 =============================================================================== 1905 ===============================================================================
1906 1906
1907 More details on the `scanpy documentation 1907 More details on the `scanpy documentation
1908 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups.html>`__ 1908 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups.html>`__
1909 1909
1910 Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`) 1910 Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`)
1911 ================================================================================== 1911 ==================================================================================
1912 1912
1913 More details on the `scanpy documentation 1913 More details on the `scanpy documentation
1914 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_violin.html>`__ 1914 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_violin.html>`__
1915 1915
1916 Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`) 1916 Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`)
1917 ==================================================================================== 1917 ====================================================================================
1918 1918
1919 More details on the `scanpy documentation 1919 More details on the `scanpy documentation
1920 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_dotplot.html>`__ 1920 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_dotplot.html>`__
1921 1921
1922 Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`) 1922 Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`)
1923 ==================================================================================== 1923 ====================================================================================
1924 1924
1925 More details on the `scanpy documentation 1925 More details on the `scanpy documentation
1926 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_heatmap.html>`__ 1926 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_heatmap.html>`__
1927 1927
1928 Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`) 1928 Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`)
1929 ========================================================================================== 1929 ==========================================================================================
1930 1930
1931 More details on the `scanpy documentation 1931 More details on the `scanpy documentation
1932 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_matrixplot.html>`__ 1932 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_matrixplot.html>`__
1933 1933
1934 Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`) 1934 Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`)
1935 ================================================================================================== 1935 ==================================================================================================
1936 1936
1937 More details on the `scanpy documentation 1937 More details on the `scanpy documentation
1938 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__ 1938 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__
1939 ]]></help> 1939 ]]></help>
1940 <expand macro="citations"/> 1940 <expand macro="citations"/>
1941 </tool> 1941 </tool>