Vince Carey vjcitn
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| library(shiny) | |
| library(xenLite) | |
| library(SpatialExperiment) | |
| what = "LUAD" | |
| ui = fluidPage( | |
| sidebarLayout( | |
| sidebarPanel( | |
| uiOutput("topbox"), |
vjcitn
/ r-dev.noload.txt
Created
September 19, 2024 02:06
error with attempt to install impute from bioc.r-universe.dev
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| setup: | |
| > options(repos=c(BioCsoft="https://bioc.r-universe.dev", CRAN="https://cloud.r-project.org")) | |
| > getOption("repos") | |
| BioCsoft CRAN | |
| "https://bioc.r-universe.dev" "https://cloud.r-project.org" | |
| > install.packages("impute") | |
| Installing package into ‘/Users/papa/Library/R/arm64/4.4/library’ |
vjcitn
/ ggplot_seg.R
Created
September 1, 2024 21:06
code that uses ggplot and some cell-level summaries on XenSPEP/XenSCE
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| library(plotly) | |
| library(ggplot2) | |
| library(XenSCE) | |
| if (!exists("gbm")) load("gbm.rda") | |
| print.xen_ggprep = function(x, ...) { | |
| cat(sprintf("xen_ggprep instance for %d cells with %d cell boundary vertices.\n", ncol(x$sampd), nrow(x$bounds))) | |
| } | |
| ggprep_seg = function(xsce, xlim=c(5800,6200), ylim=c(6300, 6700), show_tx=TRUE) { |
vjcitn
/ plotly_seg.R
Created
August 31, 2024 17:05
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| library(plotly) | |
| library(ggplot2) | |
| library(XenSCE) | |
| if (!exists("gbm")) load("gbm.rda") | |
| plotly_seg = function(xsce, xlim=c(5800,6000), ylim=c(6300, 6500), show_tx=TRUE) { | |
| bounds = getCellBoundaries(xsce) | |
| bounds = bounds[bounds$vertex_x > xlim[1] & | |
| bounds$vertex_x < xlim[2] & bounds$vertex_y > ylim[1] & bounds$vertex_y < ylim[2],] | |
| c4 <- as.data.frame(bounds) | |
| #ggplot(c4, aes(x=vertex_x, y=vertex_y, group=cell_id)) + geom_path() -> pas |
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| library(shiny) | |
| library(ParquetDataFrame) | |
| library(XenSCE) | |
| if (!exists("gbm")) load("gbm.rda") | |
| ui = fluidPage( | |
| sidebarLayout( | |
| sidebarPanel( | |
| helpText("view gbm"), |
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| get_bioc_packagelist = function(rel = "RELEASE_3_19") { | |
| system("git clone https://git.bioconductor.org/admin/manifest") | |
| owd = getwd() | |
| setwd("manifest") | |
| on.exit(setwd(owd)) | |
| system(paste("git checkout ", rel)) | |
| proc_software.txt = function() { | |
| x = readLines("software.txt")[-1] # first line is comment | |
| nn = which(nchar(x)==0) | |
| tmp = x[-nn] |
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| library(EBImage) | |
| library(shiny) | |
| ui = fluidPage( | |
| sidebarLayout( | |
| sidebarPanel( | |
| helpText("EBImage explorer"), | |
| fileInput("inimg", "file"), | |
| numericInput("scalefactor", "multfac", min=1, max=50, value=10,step=1), | |
| sliderInput("blursig", "sigma for blur", min=1, max=100, value=50) |
vjcitn
/ filter_gtex.txt
Created
August 10, 2024 11:48
script for filtering a gtex resource from https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/imported/GTEx_V8/ge/
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| #tabix Lung.tsv.gz 1:1-300000000 > lung.chr1.tsv | |
| #tabix Lung.tsv.gz 2:1-300000000 > lung.chr2.tsv | |
| #tabix Lung.tsv.gz 3:1-300000000 > lung.chr3.tsv | |
| #tabix Lung.tsv.gz 4:1-300000000 > lung.chr4.tsv | |
| #tabix Lung.tsv.gz 5:1-300000000 > lung.chr5.tsv | |
| #tabix Lung.tsv.gz 6:1-300000000 > lung.chr6.tsv | |
| #tabix Lung.tsv.gz 7:1-300000000 > lung.chr7.tsv | |
| #tabix Lung.tsv.gz 8:1-300000000 > lung.chr8.tsv | |
| #tabix Lung.tsv.gz 9:1-300000000 > lung.chr9.tsv | |
| #tabix Lung.tsv.gz 10:1-300000000 > lung.chr10.tsv |
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| # retrieve these from https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenData/ | |
| #-rw-r--r-- 1 exouser exouser 3300521324 Mar 20 21:17 transcripts.parquet | |
| #-rw-r--r-- 1 exouser exouser 68454210 Mar 20 21:16 nucleus_boundaries.parquet | |
| #-rw-r--r-- 1 exouser exouser 73791358 Mar 20 21:15 cell_boundaries.parquet | |
| #-rw-r--r-- 1 exouser exouser 242459483 Apr 10 03:46 cell_feature_matrix.tar.gz | |
| #-rw-r--r-- 1 exouser exouser 44907408 Mar 20 21:15 cells.csv.gz | |
| # tar zxf cell_feature_matrix.tar.gz to obtain folder cell_feature_matrix | |
| library(Matrix) |
vjcitn
/ explore_bert.R
Last active
July 17, 2024 13:35
look at 'safetensors' component of bert (use after usebert.R succeeds)
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| # probe R user cache file system for bert resources | |
| explore_bert = function() { | |
| if (!requireNamespace("tibble")) stop("please install tibble to use this function") | |
| res = dir(tools::R_user_dir("../huggingface/hub/models--google-bert--bert-base-uncased/snapshots/", "cache"), full=TRUE, recursive=TRUE) | |
| if (length(res)<1) stop("not finding huggingface/hub or bert components in cache") | |
| safetpath = grep("model.safetensors", res, value=TRUE) | |
| st = try(reticulate::import("safetensors")) | |
| if (inherits(st, "try-error")) stop("can't import safetensors with reticulate") | |
| oo = st$safe_open(filename=safetpath, framework="pt") | |
| kk = oo$keys() |
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