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https://github.com/alleninstitute/scrattch.vis
scRNA-seq data visualization from scrattch
https://github.com/alleninstitute/scrattch.vis
data-visualization r scrattch transcriptomics
Last synced: 17 days ago
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scRNA-seq data visualization from scrattch
- Host: GitHub
- URL: https://github.com/alleninstitute/scrattch.vis
- Owner: AllenInstitute
- License: other
- Created: 2018-03-15T18:02:17.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2024-04-10T23:09:38.000Z (9 months ago)
- Last Synced: 2024-08-31T01:08:02.520Z (4 months ago)
- Topics: data-visualization, r, scrattch, transcriptomics
- Language: R
- Size: 104 MB
- Stars: 24
- Watchers: 13
- Forks: 2
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# scrattch.vis
Single-cell RNA-seq visualization tools.
This package is under heavy development and optimization.
## Installation
All of the dependencies for `scrattch.vis` are available from CRAN. You can install scrattch.vis from Github using:
```
install.packages("devtools")
devtools::install_github("AllenInstitute/scrattch.vis")
```
## Plot Types
Once installed, `scrattch.vis` provides a variety of functions for visualizing scRNA-seq data based on sample annotations. Each of these returns a `ggplot2` plot object:
Load packages and data:
```
library(tasic2016data)
library(scrattch.vis)
options(stringsAsFactors = F)
anno <- tasic_2016_anno
anno <- anno[anno$primary_type_id > 0,]
data <- tasic_2016_rpkm
data_df <- cbind(sample_name = colnames(data),
as.data.frame(t(data[c("Pvalb","Sst","Rorb"),])))
```
### Sample-centric plots:
sample_bar_plot()
```
sample_bar_plot(data_df,
anno,
genes = c("Pvalb","Sst","Rorb"),
grouping = "primary_type",
group_order = c(1,6,2,9,4),
log_scale = FALSE,
font_size = 5,
label_type = "angle")
```
sample_heatmap_plot()
```
sample_heatmap_plot(data_df,
anno,
genes = c("Pvalb","Sst","Rorb"),
grouping = "primary_type",
log_scale = TRUE,
font_size = 5)
```
sample_fire_plot()
```
sample_fire_plot(data_df,
anno,
genes = c("Pvalb","Sst","Rorb"),
grouping = "primary_type",
log_scale = TRUE,
top_value = "lowest",
font_size = 5)
```
### Group-centric plots:
group_violin_plot()
```
group_violin_plot(data_df,
anno,
genes = c("Pvalb","Sst","Rorb"),
grouping = "primary_type",
log_scale = FALSE,
font_size = 5,
rotate_counts = TRUE)
```
group_quasirandom_plot()
```
group_quasirandom_plot(data_df,
anno,
genes = c("Pvalb","Sst","Rorb"),
grouping = "primary_type",
log_scale = FALSE,
font_size = 5,
rotate_counts = TRUE)
```
group_dot_plot()
```
group_dot_plot(data_df,
anno,
genes = c("Pvalb","Sst","Rorb"),
grouping = "primary_type",
log_scale = TRUE,
font_size = 5,
max_size = 5,
rotate_counts = TRUE)
```
group_box_plot()
```
group_box_plot(data_df,
anno,
genes = c("Pvalb","Sst","Rorb"),
grouping = "primary_type",
log_scale = FALSE,
font_size = 5,
rotate_counts = TRUE)
```
group_heatmap_plot()
```
group_heatmap_plot(data_df,
anno,
genes = c("Pvalb","Sst","Rorb"),
grouping = "primary_type",
stat = "tmean",
log_scale = TRUE,
font_size = 5,
rotate_counts = TRUE)
```
## The `scrattch` suite
`scrattch.vis` is one component of the [scrattch](https://github.com/AllenInstitute/scrattch/) suite of packages for Single Cell RNA-seq Analysis for Transcriptomic Type CHaracterization from the Allen Institute.
## License
The license for this package is available on Github at: https://github.com/AllenInstitute/scrattch.vis/blob/master/LICENSE
## Level of Support
We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests.
## Contribution Agreement
If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in full at: https://github.com/AllenInstitute/scrattch.vis/blob/master/CONTRIBUTION