In celsomilne/scSpatial: Single-Cell Spatial Data

library(BiocStyle)
knitr::opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE)

Downloading the Data

First, we download the data from Harvard

library(BiocFileCache)
bfc <- BiocFileCache("raw_data", ask=FALSE)
data.url <- "http://lincs.hms.harvard.edu/db/datasets/20236/results?search=&output_type=.csv"

data.path <- bfcrpath(bfc, data.url)

Now read it into our session.

library(tidyverse)
data <- read_csv(data.path)

Now, we want to clean the data up a bit.

data <- data %>%
  rename(cellID="Cell ID Number",
         imageID="Raw Image",
         x="X-coordinate", 
         y="Y-coordinate",
         small_mol_name="Small Molecule Name", 
         small_mol_conc="Small Mol Concentration",
         conc_unit="Small Mol Conc Unit",
         cycif_round="CycIF Round", 
         primary_antibody="Primary Antibody Name",
         secondary_antibody="Secondary Antibody Name",
         cytell_filter="Cytell filter",
         protein="Protein Detected Name",
         other_detected="Other Reagent Detected Name",
         intensity="Measured Fluorescence Intensity (a.u.)",
         well="Well",
         field="Field",
         shape_area="Cell Area (um^2)",
         shape_perimiter="Cell Perimeter (um)",
         shape_circularity="Cell Circularity") %>%
  select(-"Registered Image", -"Cell Name", -"Well_1") %>%
  select(!matches(".*(LINCS|Timepoint).*")) %>%
  mutate(cellID=factor(paste(imageID, cellID, sep="_")),
         imageID=factor(imageID),
         protein=str_replace(protein, " ", "_"),
         small_mol_name=factor(small_mol_name),
         conc_unit=factor(conc_unit),
         primary_antibody=factor(primary_antibody),
         secondary_antibody=factor(secondary_antibody),
         cytell_filter=factor(cytell_filter),
         other_detected=factor(other_detected),
         cycif_round=factor(cycif_round),) %>%
  spread(protein, intensity, sep="_")

Save to ExperimentHub Storage

Prepare all the files for storage on the ExperimentHub.

path <- file.path("scSpatial", "Lin-Melanoma", "1.0")
dir.create(path, showWarnings=FALSE, recursive=TRUE)

saveRDS(data, file=file.path(path, "spatialCellData.rds"))

And get rid of the temporary folder and the cache.

unlink(temp, recursive=TRUE, force=TRUE)
unlink("raw_data", recursive=TRUE, force=TRUE)

celsomilne/scSpatial documentation built on Aug. 11, 2020, 9:51 a.m.