Vince Carey vjcitn
vjcitn
/ gist:4e6af8b67103e78d599b104b091c0abe
Created
March 2, 2025 11:13
AnnotationPipeline step -- from preliminary sqlite to sanctionedSqlite for a single organism
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| # This function can be run in a 'newPkgs' folder after sufficient | |
| # results have been obtained in annosrc/db, to produce a sanctionedSqlite database | |
| # for a single organism | |
| # the following constants are crucial | |
| whattype <- tolower("OrgDb") | |
| wheretoput <- 20250301 | |
| theversion <- "3.21.0" |
vjcitn
/ chkInclusion.R
Created
February 16, 2025 22:18
extraction of shapes and counts of transcripts within shape boundaries
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| library(SpatialData) | |
| library(SpatialData.data) | |
| library(sf) | |
| library(SummarizedExperiment) | |
| if (!exists("mb")) mb = MouseBrainMERFISH() | |
| make_circles = function(spd, shapetype="cells") { | |
| cshape = SpatialData::shapes(spd)[[shapetype]] | |
| df1 = data(cshape) |> as.data.frame() |
vjcitn
/ gist:c2a7d034b84cfc33ee1e9e3b1f9354c7
Created
February 16, 2025 18:58
code for producing sf ellipse geometry from data frame with center, lengths of major/minor radii, and orientation angle in degrees
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| df2ellipses = function(datf, npts=100) { | |
| requireNamespace("sfdep") | |
| requireNamespace("sf") | |
| stopifnot(all(c("X_centroid", "Y_centroid", "maj", "min", "angdeg") %in% names(datf))) | |
| dd = data.matrix(datf[,c("X_centroid", "Y_centroid")]) | |
| cens = lapply(seq_len(nrow(datf)), function(x) sf::st_point(dd[x,])) | |
| maj = datf$maj | |
| min = datf$min | |
| angle_in_deg = datf$angdeg # angle_in_rad/0.01745329 | |
| dd = data.matrix(cbind(dd, angdeg=datf[,"angdeg"])) #angle_in_deg) |
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| library(shiny) | |
| library(SpatialData) | |
| library(SpatialData.plot) | |
| library(SpatialData.data) | |
| library(ggmap) | |
| library(ggplot2) | |
| library(sf) | |
| if (!exists("brdat")) brdat = Breast2fov_10x() |
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| library(SpatialData) | |
| library(SpatialData.data) | |
| library(sf) | |
| library(ggplot2) | |
| if (!exists("br")) br = Breast2fov_10x() | |
| brsh = shape(br) | |
| library(SpatialData.plot) | |
| # some points to form a subregion | |
| pick = structure(list(x = c(355.185319678255, 353.624236083554, 510.140679646861, |
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| make_parq_url = function(stub) { | |
| stub = sub("parquet$", "", stub) | |
| sprintf("https://mghp.osn.xsede.org/bir190004-bucket01/BiocParquetAnno/%s.parquet", stub) | |
| } | |
| if (!dbIsValid(con)) con = dbConnect(duckdb()) | |
| query_osn = function(con, stub="gene_info") { | |
| url = make_parq_url(stub) | |
| dbExecute(con, "INSTALL httpfs from core_nightly;") |
vjcitn
/ gist:dd7ec30c239de685e5e1cd4b98edbc37
Created
November 22, 2024 11:54
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| --- | |
| title: "`Some SpatialData visualizations`" | |
| date: "`r format(Sys.Date(), '%B %d, %Y')`" | |
| package: "`r BiocStyle::pkg_ver('SpatialData')`" | |
| author: | |
| - name: Helena Lucia Crowell | |
| - name: Louise Deconinck | |
| - name: Artür Manukyan | |
| - name: Dario Righelli | |
| - name: Estella Dong |
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| trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/parody_1.65.0.tar.gz' | |
| Content type 'application/x-gzip' length 499981 bytes (488 KB) | |
| ================================================== | |
| downloaded 488 KB | |
| Error: ERROR: no permission to install to directory ‘/usr/local/lib/R/host-site-library’ |
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| <?xml version="1.0"?> | |
| <Ontology xmlns="http://www.w3.org/2002/07/owl#" | |
| xml:base="http://www.semanticweb.org/vincent/ontologies/2024/7/untitled-ontology-10" | |
| xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" | |
| xmlns:xml="http://www.w3.org/XML/1998/namespace" | |
| xmlns:xsd="http://www.w3.org/2001/XMLSchema#" | |
| xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" | |
| ontologyIRI="http://www.semanticweb.org/vincent/ontologies/2024/7/untitled-ontology-10"> | |
| <Prefix name="" IRI="http://www.semanticweb.org/vincent/ontologies/2024/7/untitled-ontology-10/"/> | |
| <Prefix name="owl" IRI="http://www.w3.org/2002/07/owl#"/> |
vjcitn
/ install_py_events.txt
Created
October 23, 2024 21:29
log of reticulate::install_python events
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| > reticulate::install_python(version="3.12") | |
| trying URL 'https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer' | |
| Content type 'text/plain; charset=utf-8' length 2827 bytes | |
| ================================================== | |
| downloaded 2827 bytes | |
| Installing pyenv ... | |
| Cloning into '/home/stvjc/.local/share/r-reticulate/pyenv'... | |
| remote: Enumerating objects: 1289, done. | |
| remote: Counting objects: 100% (1289/1289), done. |