diff --git a/subdomains/singlecell/sections/1_beginner.yml b/subdomains/singlecell/sections/1_beginner.yml index 68c7b924..b8346fec 100644 --- a/subdomains/singlecell/sections/1_beginner.yml +++ b/subdomains/singlecell/sections/1_beginner.yml @@ -110,6 +110,72 @@ tabs: button_icon: tutorial button_tip: View tutorial + - id: data_viz + title: Visualising Data + heading_md: > + There are a few key tools for visualising single-cell data in Galaxy. + content: + - title_md: Plot with Scanpy + description_md: > + Plot with Scanpy + This tool allows you to generate many plots, from scatterplots, to violin plots, to gene heatplots. + inputs: + - anndata + - hdf5 + button_link: "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot" + button_icon: tool + button_tip: Run tool + + - title_md: Scanpy PlotEmbed + description_md: > + Scanpy PlotEmbed + This tool allows you to plot embeddings like UMAPs. + inputs: + - anndata + - hdf5 + button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed" + button_icon: tool + button_tip: Run tool + + - title_md: Scanpy PlotTrajectory + description_md: > + Scanpy PlotTrajectory + This tool allows you to plot trajectory data, such as PAGA, pre-calculated in an AnnData object. + inputs: + - anndata + - hdf5 + button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_trajectory/scanpy_plot_trajectory" + button_icon: tool + button_tip: Run tool + + - title_md: Scanpy Plot dimension reduction + description_md: > + Scanpy Plot dimension reduction + This tool allows you to plot embeddings such as PCA, UMAP, and tSNE. + inputs: + - RDS with a Seurat Object + - Single Cell Experiment + - Seurat H5 + - Loom + - AnnData + button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_dim_plot/seurat_dim_plot" + button_icon: tool + button_tip: Run tool + + - title_md: Plot with Seurat + description_md: > + Plot with Seurat + This tool allows you to plot gene expressions, such as with Violin Plots. + inputs: + - RDS with a Seurat Object + - Single Cell Experiment + - Seurat H5 + - Loom + - AnnData + button_link: "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot" + button_icon: tool + button_tip: Run tool + - id: help title: Help content: