This is the base plot for superimposing annotations like cell types, cluster assignments, and measured activities.

plot_dims(df, x, y, color = "cell_id", size = 0.1, alpha = 1, palette = "cloupe", labels = NULL, label_legend = TRUE, label_groups = FALSE)

df | plot data |
---|---|

x | variable for x-axis |

y | variable for y-axis |

color | variable for point colors (default is black) |

size | size for |

alpha | alpha for |

palette | palette for continuous colors. One of cloupe (the default), brewer, viridis. |

labels | labels for groups |

label_legend | add labels to legend |

label_groups | add labels to points |

Embeddings can be calculated by `calc_umap()`

and `calc_tsne()`

, and
retrieved with `tidy_dims()`

.

Other plot functions: `plot_activity`

,
`plot_hairpin_coverage`

plot_dims(fsce_tidy, UMAP1, UMAP2, size = 1)plot_dims(fsce_tidy, UMAP1, UMAP2, IL7R, size = 1)plot_dims(fsce_tidy, UMAP1, UMAP2, Uracil_45, size = 1)plot_dims(fsce_tidy, UMAP1, UMAP2, k_cluster, size = 1)plot_dims(fsce_tidy, UMAP1, UMAP2, k_cluster, labels = LETTERS[1:6])plot_dims(fsce_tidy, UMAP1, UMAP2, k_cluster, labels = LETTERS[1:6], label_groups = TRUE)