Plotting: pl

Plotting: pl#

The plotting module dotools_py.pl contains a collection of functions for enhance visualization of sc/snRNA-seq data.

Categorical plots#

pl.barplot(adata, x_axis, feature[, ...])

Barplot with statistical significance.

pl.violinplot(adata, x_axis, feature[, hue, ...])

Violin plot with statistical significance.

pl.boxplot(adata, x_axis, feature[, ...])

Boxplot with statistical significance.

pl.lineplot(adata, x_axis, features[, hue, ...])

Lineplot for AnnData.

pl.ridgeplot(adata, group_by, feature[, ...])

Ridgeplot for AnnData.

Embeddings plots#

pl.embedding(adata, color[, split_by, ...])

Scatterplot for an embedding.

pl.split_embedding(adata, split_by[, ...])

Scatter plot splitting categorical data in an embedding.

pl.umap(adata, color[, split_by, ...])

Scatter plot in UMAP basis.

pl.density(adata, color[, figsize, ax, ...])

Density plot.

Matrix plots#

pl.dotplot(adata, x_axis, features[, ...])

Makes a 2d dotplot or 3d dotplot.

pl.heatmap(adata, group_by, features[, ...])

Heatmap of the mean expression of genes across a groups.

pl.heatmap_foldchange(adata, group_by, ...)

Heatmap of the log2-foldchange of genes across a groups between two conditions.

Statistical plots#

pl.cell_composition(adata, annot_key, ...[, ...])

Stacked barplot showing changes in cell-type proportions.

pl.split_bar_gsea(df, term_col, col_split, ...)

Split BarPlot for GO terms.

pl.correlation(adata[, group_by, figsize, ...])

Calculate correlation between samples.

pl.volcano_plot(df[, lfc_col, pval_col, ...])

Generate a volcano plot.

Visium#

These functions allow the visualisation for AnnData containing spatial transcriptomics (Visium) data.

pl.slides(adata, color[, batch_key, ncols, ...])

Plot visium slides.

pl.layers(adata, color, key_layers[, ncols, ...])

Plot several layers.

Classes#

These classes allow to calculate and add statistical information to bar-, box- and violin-plots.

pl.TestData(data, feature, cond_key, ctrl, ...)

Class to perform test in AnnData or Pandas DataFrames.

pl.StatsPlotter(axis, x_axis, y_axis, ctrl, ...)

Class to add statistics on bar, box or violin plots.