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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r setup1, include=FALSE}
knitr::opts_chunk$set(fig.path=".readme_files/", warning=FALSE, message=FALSE, error=FALSE, echo = TRUE)
```
<a href="https://travis-ci.org/dynverse/dynplot"><img src="https://travis-ci.org/dynverse/dynplot.svg" align="left"></a> <a href="https://codecov.io/gh/dynverse/dynplot"> <img src="https://codecov.io/gh/dynverse/dynplot/branch/master/graph/badge.svg" align="left" /></a> [**ℹ️ Tutorials**](https://dynverse.org) [**ℹ️ Reference documentation**](https://dynverse.org/reference/dynplot) <br><img src="man/figures/logo.png" align="right" />
# Common visualisation tools for single-cell trajectories
## Installation
```r
devtools::install_github("dynverse/dynplot")
```
On linux, udunits2 has to be installed:
* Debian / Ubuntu / Linux mint: `sudo apt-get install libudunits2-dev`
* Fedora / CentOS: `sudo dnf install udunits2-devel`
## Usage
The package provides different ways to plot both the topology and cellular properties of a trajectory:
```{r, echo=FALSE}
library(dplyr)
library(dynplot)
library(dynutils)
library(dynwrap)
library(tidyverse)
library(patchwork)
data(example_bifurcating)
trajectory <- example_bifurcating
trajectory <- trajectory %>% add_root()
grouping <- trajectory$prior_information$groups_id
groups <- tibble(dynwrap::group_onto_nearest_milestones(trajectory)) %>%
mutate(color=dynplot:::milestone_palette_list$auto(n()))
features_oi <- apply(as.matrix(trajectory$counts), 2, sd) %>% sort() %>% names() %>% tail(10)
feature_oi <- features_oi[[10]]
```
```{r cells, fig.width=15, fig.height=10, echo=FALSE}
empty <- ggplot() + theme_void()
question <- empty + geom_text(aes(0, 0, label="????"))
unavailable <- empty + geom_text(aes(0, 0, label="----"))
title <- list(
dynplot:::empty_plot(),
# empty + geom_label(aes(0, 0, label="Topology")),
empty + geom_label(aes(0, 0, label="Ordering")),
empty + geom_label(aes(0, 0, label="Grouping/clustering")),
empty + geom_label(aes(0, 0, label="Expression of \n a single gene")),
empty + geom_label(aes(0, 0, label="Pseudotime"))
)
dendro <- list(
empty + geom_label(aes(0, 0, label="Dendrogram")),
# plot_dendro(trajectory),
plot_dendro(trajectory, "milestone"),
plot_dendro(trajectory, grouping=grouping, groups=groups),
plot_dendro(trajectory, feature_oi=feature_oi),
plot_dendro(trajectory, "pseudotime")
)
onedim <- list(
empty + geom_label(aes(0, 0, label="Onedim")),
# plot_onedim(trajectory),
plot_onedim(trajectory, "milestone"),
plot_onedim(trajectory, grouping=grouping, groups=groups),
plot_onedim(trajectory, feature_oi=feature_oi),
plot_onedim(trajectory, "pseudotime")
)
graph <- list(
empty + geom_label(aes(0, 0, label="Graph")),
# plot_graph(trajectory),
plot_graph(trajectory, "milestone"),
plot_graph(trajectory, grouping=grouping, groups=groups),
plot_graph(trajectory, feature_oi=feature_oi),
plot_graph(trajectory, "pseudotime")
)
dimred <- list(
empty + geom_label(aes(0, 0, label="Dimensionality reduction")),
# plot_dimred(trajectory),
plot_dimred(trajectory, "milestone"),
plot_dimred(trajectory, grouping=grouping, groups=groups),
plot_dimred(trajectory, feature_oi=feature_oi),
plot_dimred(trajectory, "pseudotime")
)
wrap_plots(
c(title, dendro, onedim, graph, dimred),
nrow=5,
byrow=TRUE
) & theme(legend.position = "none")
```
And to plot the expression and feature importances of many genes along the trajectory
```{r heatmap, echo=FALSE, fig.width=10, fig.height=6}
cell_feature_importance <- dynfeature::calculate_cell_feature_importance(trajectory %>% dynwrap::add_waypoints())
plot_heatmap(trajectory, grouping = trajectory$prior_information$grouping_assignment)
```
## Latest changes
Check out `news(package = "dynwrap")` or [NEWS.md](inst/NEWS.md) for a full list of changes.
<!-- This section gets automatically generated from inst/NEWS.md, and also generates inst/NEWS -->
```{r news, echo=FALSE, results="asis"}
dynutils::update_news()
cat(dynutils::recent_news())
```
## Dynverse dependencies
<!-- Generated by "update_dependency_graphs.R" in the main dynverse repo -->
