Open lgatto opened 6 years ago
Following up on this a newer more reliable verion is available here: https://github.com/tkonopka/umap
umap
is now available in CRAN
## Install and load umap package
install.packages("umap")
library("umap")
## Load example dataset
library("pRolocdata")
data("hyperLOPIT2015")
## create UMAP visualisation
hl.umap <- umap(exprs(hyperLOPITU2OS2018))
## Pass projections matrix to plot2D
xx <- (hl.umap$layout)
plot2D(xx, fcol = "markers", method = "none",
methargs = list(hyperLOPITU2OS2018),
main = "UMAP - hyperLOPIT2018")
@ococrook - any opinion on these different R packages:
ropenscilabs/umapr
.tkonopka/umap
, including R and python implementations - this package also allows to project data onto an existing embedding, which is a useful feature.jlmelville/uwot
.umap seems the most reliable - already on CRAN etc - well tested. Likely to be well developed in the future. The code looks better written as well.
I'm closing this issue but happy to get a PR that add UMAP.
I have written code to add UMAP as an option to plot2D
and tested some default parameters that work well with quantitative proteomics data. This uses the umap
function from the umap
package in CRAN. which Olly suggested several years ago. I still think this looks like the best option.
I was thinking it would be nice to have a vignette dedicated to plot2D
and how to customise plots. Will open a separate issue for this to discuss.
Plan to submit a PR for UMAP shortly if you are still happy for a PR. Will also wait to hear from you regarding #152
CC @Charl-Hutchings
See https://github.com/ropenscilabs/umapr