Plots: plt#
Import Stereopy :
import stereo as st
Here supports both static and interactive plotting modes to visualize our analysis results vividly.
Plot Collection#
The plot collection for StereoExpData object.
Plot the cells. |
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Spatial distribution ofter scatter. |
Draw the spatial distribution of expression quantity of the gene specified by gene names, just only for Gaussian smoothing, inluding the raw and smoothed. |
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Quality control index distribution visualization. |
Scatter of highly variable genes |
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Visualize module scores with spatial position. |
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Plot hotspot modules |
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Interactive spatial scatter after clustering. |
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Interactive spatial distribution. |
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Interactive spatial scatter after clustering. |
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Volcano plot of maker genes. |
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Heatmap plot of maker genes. |
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Scatter plot of maker genes. |
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Scatter of marker genes |
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Spatial distribution of |
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Draw the spatial distribution of expression quantity of the gene specified by gene names. |
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Scatter plot of UMAP after reducing dimensionalities. |
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Violin plot to show index distribution of quality control. |
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Generate dot plot based on the result of CellCellCommunication. |
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Heatmap of number of interactions in each cluster pairs. |
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Circos plot of number of interactions in each cluster pairs. |
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Sankey-plot showing inter- and/or intra-cellular gene interaction. |
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Plot heatmap for Regulon specificity scores (RSS) value |
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Plot heatmap for auc value for regulons |
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Intuitive way of visualizing how feature expression changes across different identity classes (clusters). |
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Plot genes of one regulon on a 3D map |
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Plot genes of one regulon on a 2D map |
Visualize the co-occurence by line plot; each subplot represent a celltype, each line in subplot represent the co-occurence value of the pairwise celltype as the distance range grow. |
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Visualize the co-occurence by heatmap; each subplot represent a certain distance, each heatmap in subplot represent the co-occurence value of the pairwise celltype. |
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abstract paga plot for the paga result. |
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abstract paga plot for the paga result and cell distribute around paga. |
Plots a dendrogram using the precomputed dendrogram information stored in |
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Scatter representing mean expression of genes on each cell cluster. |
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Heatmap representing mean expression of genes on each cell cluster. |
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show a boxplot of a specific gene expression in branch of use_col |
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Use fuzzy C means cluster method to cluster genes based on 1-p_value of celltypes in branch |
spatial trajectory plot for paga in time_series multiple slice dataset |
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a line plot to show the trend of each cluster of fuzzy C means |
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a tree plot to display the cell amounts changes during time series, trajectory can be add to plot by edges. |
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spatial trajectory plot for paga in time_series multiple slice dataset |
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Plot elbow for pca. |
Distribution of expression count of marker genes along with pseudotime |
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Plot vectors or streams of pseudo-time. |
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Spatial distribution of pseudotime. |
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Plot vector field of cell trajectories embodied in 3D space. |