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an instance of the Orchestrating Spatial Transcriptomics Analysis book
Jun 8 2026: use us.gcr.io/broad-dsp-gcr-public/terra-base:1.0.1 to have sudo capabilities.
To install the infrastructure, et a machine with 4 CPUs and 150 GB disk.
We use r2u to get packages and ubuntu infrastructure. Specifically, we use the script
#!/bin/bash
| #' sfe_efa_bridge.R | |
| #' | |
| #' Bridge between SpatialFeatureExperiment cell boundary polygons | |
| #' and Elliptic Fourier Analysis (Momocs). | |
| #' | |
| #' Extracts cell segmentation polygons from an SFE object, | |
| #' computes EFA coefficients per cell, stores them as a | |
| #' reducedDim or colData, and provides reconstruction/visualization. | |
| #' | |
| #' Dependencies: |
| # Set seed for reproducibility | |
| set.seed(123) | |
| # Generate 15 uniform points in the unit circle | |
| n <- 15 | |
| # Method: Generate points uniformly in unit circle using polar coordinates | |
| # We need to use square root to ensure uniform distribution | |
| r <- sqrt(runif(n)) # Square root to get uniform distribution | |
| theta <- runif(n, 0, 2*pi) |
| library(shiny) | |
| library(plotly) | |
| library(SpatialData) | |
| library(SpatialData.plot) | |
| library(ggplot2) | |
| load("abund500.rda") | |
| gene_choices <- sort(abund500) | |
| dd <- readSpatialData("data.zarr", images = FALSE) |
| > library(ellmer) | |
| 1/4 packages newly attached/loaded, see sessionInfo() for details. | |
| > ch = chat_ollama(model="qwen3-coder:30b") | |
| > ch$chat("Discuss how to evaluate the integral of the Gaussian density function over the whole real line.") | |
| # Evaluating the Gaussian Integral over the Entire Real Line | |
| The integral of the Gaussian density function over the whole real line is a fundamental result in mathematics and | |
| statistics: | |
| $$\int_{-\infty}^{\infty} e^{-x^2/2} dx = \sqrt{2\pi}$$ |
| library(littleDeep) | |
| library(processx) | |
| tf = tempfile() | |
| fstr = paste0(">>", tf) | |
| #file.create(tf) | |
| basecmd = sprintf("/Users/vincentcarey/INSTRUMENTATION/macmon/target/release/macmon") | |
| pp = process$new(basecmd, c("pipe"), stdout=fstr) | |
| suppress_keras_warnings() | |
| r1 = run_cifar100(nEpochs=3) | |
| pp$kill() |
| #> dput(dev) | |
| alogit = function(x) exp(x)/(1+exp(x)) | |
| dev = function (y, x) | |
| function(b) { | |
| phat = alogit(x %*% b) | |
| -2 * sum(y * log(phat) + (1 - y) * (log(1 - phat))) | |
| } | |
| Y = 1*(iris$Species == "virginica") | |
| X = data.matrix(cbind(1., iris[,1:4])) |
| available_sdio produces: | |
| > reticulate::py_last_error() | |
| ── Python Exception Message ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
| Traceback (most recent call last): | |
| File "C:\Users\stvjc\AppData\Local\R\win-library\4.6\reticulate\python\rpytools\loader.py", line 122, in _find_and_load_hook | |
| return _run_hook(name, _hook) | |
| ^^^^^^^^^^^^^^^^^^^^^^ | |
| File "C:\Users\stvjc\AppData\Local\R\win-library\4.6\reticulate\python\rpytools\loader.py", line 96, in _run_hook | |
| module = hook() |
| library(GenomicState) | |
| library(RSQLite) | |
| library(txdbmaker) | |
| hgenc49 = gencode_txdb( | |
| version = "49", | |
| genome = c("hg38"), | |
| chrs = paste0("chr", c(seq_len(22), "X", "Y", "M")) | |
| ) | |
| hgenc49$conn # 'path' is empty | |
| md = dbGetQuery(hgenc49$conn, "select * from metadata") # lacks 'Resource URL' record in metadata |