gdagstn/borges

Antique or modern atlas-like depictions of non-linear dimensionality reduction for single cell data

Hi there 👋

I am a computational biologist - originally trained as molecular biologist - who started learning data analysis in R in 2017. My current areas of expertise include transcriptomics (bulk and single cell), translatomics, neurodevelopmental disorders, neurodegenerative diseases, genome editing, and stem cell biology. I am particularly passionate about data visualization.

Since early 2021 I started honing my skills as a package developer. So fare I have released seven R packages in the wild:

• 🧠 {coldcuts} - draw and render neuroanatomical segmentations in 2D and 3D
• 🍳 {oveRlay} - annotate 2D scatterplots with overlay polygons
• 🎨 {swatcheR} - generate color swatches from pictures
• 🦜 {alamak} - let Pixel Pals handle your errors
• 🗺️ {borges} - antique cartographic style 2D point clouds (UMAP, tSNE and the like)
• 🧫 {cellula} - pipeline with wrappers to many single cell RNA-seq analysis methods
• 🏢 {HDB} - a geometric test to detect batch effects in single cell RNA-seq

with hopefully more to come.

🛠 I am currently learning three.js, a little bit of Python on the side, and Arduino physical computing as a hobby.

borges's Issues

label size

This is great. Any suggestion to change the label size without modifying the hardcoded values?

Issue regarding the labels

Hello,

I am getting the following error when I tried tun the PrepAtlas()-

labels` must have the same length as the number of points

I have added label as a character vector 2 ways but still not working. Could you please help?
progenitor1 <- DiabetesST2UMAP.combined$CellType %in% c(rep("A2.1", 100),
rep("D1", 100),
rep("A5", 100),
rep("D3", 100),
rep("A4", 100),
rep("A2", 100),
rep("D6", 100),
rep("A7", 100),
rep("A1", 100),
rep("S", 100),
rep("D2", 100),
rep("M", 100),
rep("DX", 100),
rep("I", 100),
rep("D4", 100),
rep("E", 100),
rep("D7", 100))

OR

progenitor1 <- c(rep("A2.1"),
rep("D1"),
rep("A5"),
rep("D3"),
rep("A4"),
rep("A2"),
rep("D6"),
rep("A7"),
rep("A1"),
rep("S"),
rep("D2"),
rep("M"),
rep("DX"),
rep("I"),
rep("D4"),
rep("E"),
rep("D7"))