diff --git a/.Rhistory b/.Rhistory
deleted file mode 100644
index e9be9e3..0000000
--- a/.Rhistory
+++ /dev/null
@@ -1,208 +0,0 @@
-load("C:/Users/pdanaher/Desktop/phase_ii_dataframes.RData")
-ls()
-str(norm)
-dim(norm)
-dim(raw)
-sd(rt(1000, 2))
-sd(rt(1000, 20))
-sd(rt(1000, 2000))
-sd(rt(1000, 20000))
-load("C:/Users/pdanaher/Desktop/TCGA beta hats - zilionis.RData")
-ls()
-length(betas)
-rm(list = ls())
-load("C:/Users/pdanaher/Documents/nanostring-cell-mixture-deconvolution/training matrix derivation pipeline/intermediate data/TCGA beta hats - zilionis.RData")
-ls()
-dim(betas)
-dim(betas[[1]])
-betas[[1]]
-pairs(t(betas[[1]]))
-load("C:/Users/pdanaher/Desktop/TCGA beta hats - zilionis.RData")
-names(betas)
-rownames(betas[[1]])
-load("C:/Users/pdanaher/Desktop/bc360SignatureCollection.RData")
-ls()
-str(bc360SignatureCOllection)
-library(devtools)
-install_github("NanoString-Biostats/NanoStringSignatureBase")
-install.packages("C:/Users/pdanaher/Desktop/Rpackages-master/Rpackages-master/NanoStringSignatureBase.zip", repos = NULL, type = "win.binary")
-library("NanoStringSignatureBase")
-library("NanoStringSignatureBase")
-library(NanoStringSignatureBase)
-install_github("NanoString-Biostats/Rpackages/NanoStringSignatureBase")
-install_github("Nanostring-Biostats/Rpackages/tree/master/NanoStringSignatureBase")
-install.packages("C:/Users/pdanaher/Desktop/Rpackages-master/Rpackages-master/NanoStringSignatureBase.zip", repos = NULL, type = "win.binary")
-library(NanoStringSignatureBase)
-ls()
-str(bc360SignatureCollection)
-(bc360SignatureCollection)
-load("C:/Users/pdanaher/Desktop/fibroblast_genes_gx.RData")
-ls()
-str(F)
-str(gx_fibroblast)
-str(gx_fibroblast[[1]])
-str(gx_fibroblast[[2]])
-head(gx_fibroblast[[2]])
-dim(gx_fibroblast[[2]])
-load("C:/Users/pdanaher/Documents/nanostring-cell-mixture-deconvolution/scratch space/bakeoff - residsd weighting - in progress.RData")
-ls()
-dim(betas)
-str(betas)
-head(betas[[1]][[1]])
-rowMeans(betas[[1]][[1]])
-hist(rnorm(100), breaks = 40, col = 4)
-library(NormDSP)
-?eval_protein_signal
-library(InSituSort)
-cellcols
-load("C:/Users/pdanaher/Downloads/tcga.all.mutfreqs.nosilentmuts.RData")
-ls()
-str(tcgamutfreq)
-load("C:/Users/pdanaher/Downloads/tcga.all.mutfreqs.nosilentmuts.RData")
-ls()
-temp = tcgamutfreq
-name = tmb = c()
-id = c())
-id = c()
-for (name in names(temp)){id = c(id, names(temp[[name]])); tmb = c(tmp, temp[[name]])}
-for (name in names(temp)){id = c(id, names(temp[[name]])); tmb = c(tmb, temp[[name]])}
-id = tmb = c()
-for (name in names(temp)){id = c(id, names(temp[[name]])); tmb = c(tmb, temp[[name]])}
-length(id)
-length(tmb)
-head(id)
-head(tmb)
-write.csv(cbind(id, tmb), row.names = F, file = "TMB.csv")
-getwd()
-load("C:/Users/pdanaher/Downloads/20200213_2054_RData.RData")
-ls()
-hist(apply(dfs[[2]], 2, quantile, 0.75)
-)
-hist(apply(dfs[[2]][, -1], 2, quantile, 0.75))
-load("C:/Users/pdanaher/Documents/BC360-manuscript/data/bc360 datasets.RData")
-ls()
-str(rsnorm)
-head(bcannot)
-names(annotlist)
-load("C:/Users/pdanaher/Documents/BC360-manuscript/data/bc360 datasets.RData")
-ls()
-names(annotlist)
-str(annotlist)
-load("C:/Users/pdanaher/Documents/BC360-manuscript/data_pre_pipeline/BC360 datasets/puma data.RData")
-rm(list = ls())
-load("C:/Users/pdanaher/Documents/BC360-manuscript/data_pre_pipeline/BC360 datasets/puma data.RData")
-ls()
-str(pumadata)
-names(pumadata)
-load("C:/Users/pdanaher/Documents/BC360-manuscript/data/bc360 datasets.RData")
-ls()
-str(bcannot)
-names(annotlist)
-library(NormDSP)
-??NormDSP
-data(NormDSP::mini_DSP_experiment)
-data("mini_DSP_experiment")
-ls()
-rawdata[1:10,1:10]
-head(annot)
-22*12
-setwd("C:/Users/pdanaher/Box Sync/cell signatures/manuscript/fig s1 - log linear cartoon")
-rm(list = ls())
-library(e1071)
-library(scales)
-# load TCGA LUAD:
-load("LUSC.RData")
-# linear and logscale data:
-lindat = LUSC.dat.subset$e
-logdat = log2(LUSC.dat.subset$e)
-rm(LUSC.dat.subset)
-# calculate skew for all genes, in both logscale and linear scale:
-skew.lin = apply(lindat, 2, skewness)
-skew.log = apply(logdat, 2, skewness)
-denslin = density(skew.lin[!is.na(skew.lin)])
-denslog = density(skew.log[!is.na(skew.log)])
-par(mar = c(4,4,.1,.1))
-plot(denslin, col = 0, xlab = "Skewness of genes in TCGA LUAD", ylab = "",
-cex.lab = 1.2, cex.axis = 0.7, main = "", ylim = c(0, max(denslog$y)))
-polygon(denslin, col = alpha("grey50", 0.5), border = NA)
-polygon(denslog, col = alpha("orange", 0.5), border = NA)
-legend("topright", fill = alpha(c("grey50", "orange"), 0.5),
-legend = c("Linear-scale data", "Log-transformed data"), cex = 1)
-# summary stats:
-mean(skew.lin > 2, na.rm = T)
-mean(abs(skew.log) > 2, na.rm = T)
-hist(skew.lin, col = alpha("grey50", 0.5), border = NA, ylab = "Number of genes", xlab = "Skewness",
-breaks = seq(-5,25, length.out = 100), ylim = c(0, 4000))
-hist(skew.log, add = TRUE, col = alpha("orange", 0.5), border = NA,
-breaks = seq(-5,25, length.out = 100))
-# show mean-variance relationship on logscale, linear scale:
-means.lin = apply(lindat, 2, mean)
-means.log = apply(logdat, 2, mean)
-sds.lin = apply(lindat, 2, sd)
-sds.log = apply(logdat, 2, sd)
-# summary stats:
-range(sds.lin[means.lin > 0])
-range(sds.lin[means.lin > 0])[2] / range(sds.lin[means.lin > 0])[1]
-range(sds.log, na.rm = T)
-range(sds.log, na.rm = T)[2] / range(sds.log, na.rm = T)[1]
-par(mar = c(4,4,.1,1))
-par(mfrow = c(1,2))
-plot(log2(means.lin), log2(sds.lin), log = "", xlab = "Mean", ylab = "SD",
-col = alpha("dodgerblue4", 0.05), pch = 16, xaxt = "n", yaxt = "n")
-axis(1, at = log2(10^seq(-3, 5, 2)), labels = 10^(seq(-3, 5, 2)), cex.axis = 0.65)
-axis(2, at = log2(10^seq(-15, 15, 2)), labels = 10^(seq(-15, 15, 2)), cex.axis = 0.75)
-legend("top", legend = "linear-scale data    ", bty = "n")
-lines(lowess(log(means.lin[sds.lin > 0]), log(sds.lin[sds.lin > 0])), col = "orange", lwd = 2)
-plot(means.log, sds.log, xlab = "Mean", ylab = "SD",
-col = alpha("dodgerblue4", 0.05), pch = 16, cex.axis = 0.65)
-legend("top", legend = "log2-scale data    ", bty = "n")
-lines(lowess(means.log[!is.na(sds.log)], sds.log[!is.na(sds.log)]), col = "orange", lwd = 2)
-dev.off()
-gene = "CD274"
-par(mfrow = c(1, 2))
-par(mar = c(4,4,1,.1))
-hist(lindat[, gene], breaks = 30, col = alpha("grey50", 0.5), border = NA, main = "",
-xlab = paste0("Linear-scale ", gene, " expression"), ylab = "",
-yaxt = "n", cex.axis = 0.65)
-legend("center", legend = paste0("skewness = ", round(skewness(lindat[, gene]), 1)), bty = "n")
-hist(logdat[, gene], breaks = 30, col = alpha("orange", 0.5), border = NA, main = "",
-xlab = paste0("Log-scale ", gene, " expression"), ylab = "",
-yaxt = "n", cex.axis = 0.65)
-legend("center", legend = paste0("skewness = ", round(skewness(logdat[, gene]), 1)), bty = "n")
-# histograms of CD274
-svg("gene histograms.svg", height = 3.1, width = 6)
-gene = "CD274"
-par(mfrow = c(1, 2))
-par(mar = c(4,1,1,.1))
-hist(lindat[, gene], breaks = 30, col = alpha("grey50", 0.5), border = NA, main = "",
-xlab = paste0("Linear-scale ", gene, " expression"), ylab = "",
-yaxt = "n", cex.axis = 0.65)
-legend("center", legend = paste0("skewness = ", round(skewness(lindat[, gene]), 1)), bty = "n")
-hist(logdat[, gene], breaks = 30, col = alpha("orange", 0.5), border = NA, main = "",
-xlab = paste0("Log-scale ", gene, " expression"), ylab = "",
-yaxt = "n", cex.axis = 0.65)
-legend("center", legend = paste0("skewness = ", round(skewness(logdat[, gene]), 1)), bty = "n")
-dev.off()
-setwd("~/nanostring-cell-mixture-deconvolution")
-##### this script contains the code used to build the package.
-rm(list=ls())
-setwd("~/nanostring-cell-mixture-deconvolution")
-library("devtools")
-library(roxygen2)
-setwd("InSituSort")
-devtools::document()
-devtools::document()
-devtools::document()
-devtools::test() # run unit tests
-devtools::check()
-devtools::check()
-devtools::use_vignette("my-vignette")
-usethis::use_vignette("my-vignette")
-setwd("~/nanostring-cell-mixture-deconvolution/InSituSort/vignettes")
-getwd()
-setwd("~/nanostring-cell-mixture-deconvolution")
-setwd("InSituSort")
-devtools::document()
-devtools::check()
-devtools::check()
-source('C:/Users/pdanaher/Desktop/update pandoc.R', echo=TRUE)
diff --git a/.gitignore b/.gitignore
index c066a39..631f40a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,5 @@
 inst/doc
+/.vs/SpatialDecon/v16/.suo
+.Rhistory
+/.vs/slnx.sqlite
+/.vs/VSWorkspaceState.json
diff --git a/code for creating SpatialDecon.R b/code for creating SpatialDecon.R
deleted file mode 100644
index 0432258..0000000
--- a/code for creating SpatialDecon.R	
+++ /dev/null
@@ -1,82 +0,0 @@
-##### this script contains the code used to build the package.
-rm(list=ls())
-
-### strategy for shiny-in-a-package deployment: taken from https://www.r-bloggers.com/packaging-shiny-applications-a-deep-dive/
-### code written to emulate: https://github.com/MangoTheCat/shinyAppDemo
-
-
-#### package building code: from https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/
-
-
-library("devtools")
-library(roxygen2)
-library(qpdf)
-library(BiocCheck)
-library("styler")
-#library("formatR")
-library("lintr")
-
-setwd("SpatialDecon")
-#usethis::use_tidy_style(indent_by = 4)
-#styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))
-
-devtools::document()
-devtools::test() # run unit tests
-devtools::check()
-setwd("..")
-BiocCheck("SpatialDecon")
-BiocCheckGitClone("SpatialDecon")
-setwd("SpatialDecon")
-devtools::build()
-devtools::build(binary = TRUE)
-setwd("..")
-install("SpatialDecon")
-#setwd("SpatialDecon")
-library("SpatialDecon")
-
-
-#########################################
-#### Creating data objects for SpatialDecon   ####
-#########################################
-
-# create colors:
-cellcols = c()
-cellcols["CD4.T.cells"] = "red"
-cellcols["CD8.T.cells"] = "firebrick"
-cellcols["Treg"] = "#FF66FF"
-
-cellcols["T.CD4.naive"] = "#CC0000"
-cellcols["T.CD4.memory"] = "#FF0000"
-cellcols["T.CD8.naive"] = "#FF6633"
-cellcols["T.CD8.memory"] = "#FF9900"
-
-cellcols["NK"] = "grey10"
-cellcols["B"] = "darkblue"
-cellcols["B.naive"] = "#000099"
-cellcols["B.memory"] = "#0000FF"
-cellcols["plasma"] = "#3399CC"
-cellcols["pDC"] = "#00FFFF"
-cellcols["pDCs"] = "#00FFFF"
-cellcols["macrophages"] = "#006600"
-cellcols["monocytes"] = "#33CC00"
-cellcols["monocytes.C"] = "#66CC66"
-cellcols["monocytes.NC.I"] = "#33CC00"
-cellcols["mDCs"] = "#00FF00"
-cellcols["neutrophils"] = "#9966CC"
-cellcols["mast"] = "#FFFF00"
-cellcols["fibroblasts"] = "#999999"
-cellcols["endothelial.cells"] = "#996633"
-cellcols["tumor"] = "#333333"
-
-# see how they look:
-tempb = rep(1, length(cellcols))
-names(tempb) = names(cellcols)
-barplot(tempb, las = 2, col = cellcols)
-
-
-
-save(cellcols, file = "SpatialDecon/data/cellcols.RData")
-# create test dataset:
-#source("create test results.R")
-
-
diff --git a/tests/testthat/.Rhistory b/tests/testthat/.Rhistory
deleted file mode 100644
index 36a7f2e..0000000
--- a/tests/testthat/.Rhistory
+++ /dev/null
@@ -1,251 +0,0 @@
-setwd("~/nanostring-cell-mixture-deconvolution")
-library("devtools")
-library(roxygen2)
-setwd("InSituSort")
-devtools::document()
-devtools::document()
-#usethis::use_testthat()
-devtools::test() # run unit tests
-#usethis::use_testthat()
-devtools::test() # run unit tests
-#usethis::use_testthat()
-devtools::test() # run unit tests
-#usethis::use_testthat()
-devtools::test() # run unit tests
-#usethis::use_testthat()
-devtools::test() # run unit tests
-#usethis::use_testthat()
-devtools::test() # run unit tests
-#usethis::use_testthat()
-devtools::test() # run unit tests
-#usethis::use_testthat()
-devtools::test() # run unit tests
-expect_error(sum(), NA)
-expect_error(stop(), NA)
-### test plotting functions
-test_that("florets does not error", {
-expect_error(florets(x = annot$x, y = annot$y, b = res$beta.granular[!grepl("tumor", rownames(res$beta.granular)), ],
-legendwindow = T),
-NA)
-})
-#usethis::use_testthat()
-devtools::test() # run unit tests
-?reverseDecon
-setwd("~/nanostring-cell-mixture-deconvolution")
-load("InSituSort/tests/testthat/expectedtestresults.RData")
-rm(list = ls())
-load("InSituSort/tests/testthat/expectedtestresults.RData")
-ls()
-load("191 grid decon results.RData")
-setwd("~/nanostring-cell-mixture-deconvolution")
-load("191 grid decon results.RData")
-load("191 grid decon results.RData")
-rm(list = ls())
-load("191 grid decon results.RData")
-inds = (1:15) * 20
-temprois = annot$ROI[inds]
-inds = which(is.element(annot$ROI, temprois))
-sharedgenes = intersect(rownames(safeTME), rownames(snr))
-snr = snr[c(sharedgenes, "NegProbe-Kilo"), inds]
-raw = raw[c(sharedgenes, "NegProbe-Kilo"), inds]
-rownames(raw)[rownames(raw) == "NegProbe-Kilo"] = "NegProbe"
-rownames(snr)[rownames(snr) == "NegProbe-Kilo"] = "NegProbe"
-annot = annot[inds, c("ROI", "AOI.name", "x", "y", "nuclei")]
-# save dataset for examples:
-mini_geomx_dataset = list(normalized = snr, raw = raw, annot = annot)
-save(mini_geomx_dataset, file = "InSituSort/data/mini_geomx_dataset.RData")
-# save test dataset:
-snr = snr[sharedgenes, ]
-raw = raw[sharedgenes, ]
-dim(norm)
-rm(list = ls())
-load( "InSituSort/tests/testthat/testdata.RData"))
-load( "InSituSort/tests/testthat/testdata.RData")
-load("InSituSort/tests/testthat/expectedtestresults.RData")
-ls()
-# reverse decon:
-rdres.test = reverseDecon(norm = snr,
-beta = res.test$beta,
-epsilon = 1)
-str(rdres.test)
-save(ires.test, res.test, wts.test, mergedX.test, rdres.test, file = "InSituSort/tests/testthat/expectedtestresults.RData")
-#usethis::use_testthat()
-devtools::test() # run unit tests
-setwd("~/nanostring-cell-mixture-deconvolution")
-rm(list = ls())
-#usethis::use_testthat()
-devtools::test() # run unit tests
-setwd("InSituSort")
-#usethis::use_testthat()
-devtools::test() # run unit tests
-rdres$cors
-setwd("~/nanostring-cell-mixture-deconvolution/InSituSort/tests/testthat")
-#### load test data ----------------------
-rm(list = ls())
-load("testdata.RData")
-load("expectedtestresults.RData")
-sharedgenes = intersect(rownames(safeTME), rownames(snr))
-test_that("deriveWeights is as expected", {
-wts = deriveWeights(norm = snr,
-raw = raw,
-error.model = "dsp")
-expect_true(all(abs(wts.test - wts) < 1e-3))
-})
-# merging tumor profiles:
-test_that("mergeTumorIntoX is as expected", {
-set.seed(0)
-mergedX = mergeTumorIntoX(norm = snr[sharedgenes, ],
-bg = replace(snr, TRUE, 1)[sharedgenes, ],
-pure.tumor.ids =  annot$AOI.name == "Tumor",
-X = safeTME[sharedgenes, ],
-K = 5)
-expect_true(all(abs(mergedX.test - mergedX) < 1e-3))
-})
-# insitusort:
-set.seed(0)
-ires = insitusort(Y = snr[sharedgenes, ],
-X = safeTME[sharedgenes, ],
-bg = replace(snr[sharedgenes, ], TRUE, 1),
-#method = "deconLNR",
-resid_thresh = 3, lower_thresh = 0.5)
-test_that("insitusort is as expected: beta", {
-expect_true(all(abs(ires.test$beta - ires$beta) < 1e-3))
-})
-test_that("insitusort is as expected: sigma", {
-expect_true(all(abs(ires.test$sigmas - ires$sigmas) < 1e-3))
-})
-test_that("insitusort is as expected: yhat", {
-expect_true(all(abs(ires.test$yhat - ires$yhat) < 1e-3))
-})
-test_that("insitusort is as expected: resids", {
-expect_true(all(abs(replace(ires.test$resids, is.na(ires.test$resids), 0) -
-replace(ires$resids, is.na(ires$resids), 0)) < 1e-3))
-})
-test_that("insitusort is as expected: p", {
-expect_true(all(abs(ires.test$p - ires$p) < 1e-3))
-})
-#### test insitusortTILs --------------------------------------------------
-res = insitusortTILs(norm = snr,
-raw = raw,
-bg = replace(snr, TRUE, 1),
-is_pure_tumor = annot$AOI.name == "Tumor",
-cell_counts = annot$nuclei,
-n.tumor.clusters = 5)
-### test reverse decon:
-rdres = reverseDecon(norm = snr,
-beta = res.test$beta,
-epsilon = 1)
-str(rdres)
-str(rdres.test)
-expect_true(all(abs(rdres.test$resid.sd - rdres$resid.sd) < 1e-3))
-expect_true(all(abs(rdres.test$cors - rdres$cors) < 1e-3))
-expect_true(all(abs(rdres.test$cors - rdres$cors) < 1e-3, na.rm = T))
-setwd("~/nanostring-cell-mixture-deconvolution")
-setwd("InSituSort")
-#usethis::use_testthat()
-devtools::test() # run unit tests
-expect_true(all(abs(rdres.test$resids - rdres$resids) < 1e-3))
-str(rdres.test)
-### test reverse decon:
-rdres = suppressWarnings(reverseDecon(norm = snr,
-beta = res.test$beta,
-epsilon = 1))
-test_that("reverseDecon is as expected: ", {
-expect_true(all(abs(rdres.test$resids - rdres$resids) < 1e-3))
-expect_true(all(abs(rdres.test$yhat - rdres$yhat) < 1e-3))
-expect_true(all(abs(rdres.test$coefs - rdres$coefs) < 1e-3))
-expect_true(all(abs(rdres.test$cors - rdres$cors) < 1e-3, na.rm = T))
-expect_true(all(abs(rdres.test$resid.sd - rdres$resid.sd) < 1e-3))
-})
-setwd("~/nanostring-cell-mixture-deconvolution")
-##### this script contains the code used to build the package.
-rm(list=ls())
-setwd("InSituSort")
-devtools::document()
-#usethis::use_testthat()
-devtools::test() # run unit tests
-ls
-ls()
-load("testdata.RData")
-setwd("~/nanostring-cell-mixture-deconvolution/InSituSort/tests/testthat")
-ls()
-load("testdata.RData")
-ls()
-dim(snr)
-rownames(snr)
-norm = snr
-neg.names = rownames(snr)[c(1, 540)]
-neg.names
-probepool = c(rep("a", 100), rep("b", (nrow(norm) - 100)))
-probepool
-neg.names
-negnames = neg.names
-genes = rownames(norm)
-#'
-#' Estimates per-datapoint background levels from a GeoMx experiment.
-#' In studies with two or more probe pools, different probes will have different
-#' background levels. This function provides a convenient way to account for this phenomenon.
-#'
-#' @param norm Matrix of normalized data, genes in rows and segments in columns.
-#'  Must include negprobes, and must have rownames.
-#' @param probepool Vector of probe pool names for each gene, aligned to the rows of "norm".
-#' @param negnames Names of all negProbes in the dataset. Must be at least one neg.name within each probe pool.
-#' @export
-derive_GeoMx_background_at_normalized_scale <- function(norm, probepool, negnames) {
-# check data input:
-if (nrow(norm) != length(probepool)) {
-stop("nrow(norm) != length(probepool)")
-}
-# initialize:
-bg = norm * 0
-# fill in expected background at scale of normalized data:
-for (pool in unique(probepool)) {
-# get the pool's negProbes:
-tempnegs = intersection(negnames, rownames(norm)[probepool == pool])
-if (length(tempnegs) == 0) {
-stop(paste0(pool, " probe pool didn't have any negprobes specified"))
-}
-tempnegfactor = colMeans(norm[tempnegs, , drop = F])
-# fill in the corresponding elements of bg:
-bg[probepool == pool, ] = sweep(bg[probepool == pool, ], 2, tempnegfactor, "+")
-}
-return(bg)
-}
-temp = derive_GeoMx_background_at_normalized_scale(norm = snr, probepool = probepool, negnames = negnames)
-# get the pool's negProbes:
-tempnegs = intersect(negnames, rownames(norm)[probepool == pool])
-#'
-#' Estimates per-datapoint background levels from a GeoMx experiment.
-#' In studies with two or more probe pools, different probes will have different
-#' background levels. This function provides a convenient way to account for this phenomenon.
-#'
-#' @param norm Matrix of normalized data, genes in rows and segments in columns.
-#'  Must include negprobes, and must have rownames.
-#' @param probepool Vector of probe pool names for each gene, aligned to the rows of "norm".
-#' @param negnames Names of all negProbes in the dataset. Must be at least one neg.name within each probe pool.
-#' @export
-derive_GeoMx_background_at_normalized_scale <- function(norm, probepool, negnames) {
-# check data input:
-if (nrow(norm) != length(probepool)) {
-stop("nrow(norm) != length(probepool)")
-}
-# initialize:
-bg = norm * 0
-# fill in expected background at scale of normalized data:
-for (pool in unique(probepool)) {
-# get the pool's negProbes:
-tempnegs = intersect(negnames, rownames(norm)[probepool == pool])
-if (length(tempnegs) == 0) {
-stop(paste0(pool, " probe pool didn't have any negprobes specified"))
-}
-tempnegfactor = colMeans(norm[tempnegs, , drop = F])
-# fill in the corresponding elements of bg:
-bg[probepool == pool, ] = sweep(bg[probepool == pool, ], 2, tempnegfactor, "+")
-}
-return(bg)
-}
-# get the pool's negProbes:
-tempnegs = intersect(negnames, rownames(norm)[probepool == pool])
-temp = derive_GeoMx_background_at_normalized_scale(norm = snr, probepool = probepool, negnames = negnames)
-dim(temp)
-temp[c(1:5,105:110), 1:8]
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
deleted file mode 100644
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--- a/vignettes/.gitignore
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@@ -1,2 +0,0 @@
-*.html
-*.R