Comments (2)
Hi,
If you'd like to split the plot by time (Assuming each input dataset corresponds to one time point), you could try the following customized code:
library(ggplot2)
tsne_df <- data.frame([email protected]) # After running LIGER pipeline
colnames(tsne_df) <- c("Dim1", "Dim2") # e.g. tSNE or UMAP coordinates
tsne_df[['Dataset']] <- unlist(lapply(1:length(liger_object@H), function(x) {
rep(names(liger_object@H)[x], nrow(liger_object@H[[x]]))
}))
p <- ggplot(data = tsne_df, aes(Dim1, Dim2, color=Dataset)) +
theme_bw() +
theme_cowplot(12) +
geom_point() +
labs(title = "Example Plot",
x = "Dim1", y = "Dim2") +
facet_wrap(~ Dataset)
p
Hope it helps!
Best,
from liger.
As another option I have created package scCustomize that also has some Liger functionality. I have adapted the internal Liger plotting to support Seurat like arguments including split.by
. You can check out functionality here: https://samuel-marsh.github.io/scCustomize/articles/LIGER_Functions.html
Best,
Sam
from liger.
Related Issues (20)
- "shared factor neighborhood" not used anymore as described in the paper? HOT 3
- log transform data first? HOT 1
- Another request for help regarding SCTransform HOT 1
- Generate gene and promoter bed files
- Problems with scaleNotCenter() HOT 2
- Prepare for upcoming Seurat v5 release HOT 1
- Bug in Seurat's wrapper function HOT 1
- cran package archived HOT 6
- NaNs during `SelectGenes()` HOT 1
- Error on makeFeatureMatrix HOT 1
- How to improving similarity between snRNA-seq and snATAC-seq nuclei, by tuning parameters like 'k', 'lambda'? HOT 4
- Dataset specificity plot
- Issue with loading old liger object via convertOldLiger function HOT 3
- Error in `signal_stage()` HOT 4
- invalid type "list" in R_matrix_as_sparse error HOT 3
- no slot name "defaultCluster" for this object of class "liger" HOT 1
- Query on building shared factor neighborhood graph HOT 2
- Error when performing the Wilcoxon test on the peak counts HOT 1
- Error in ImputeKNN
- How can I determine the similarity scores between clusters using Liger's UINMF? HOT 5
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from liger.