# Article workflow
library(tidyverse)
library(Seurat)
library(SingleR)
library(plotly)
# library(future)
# plan(multisession, workers=10)
options(future.globals.maxSize = 50068 * 1024^2)
library(tidyseurat)
friendly_cols <- dittoSeq::dittoColors()
# PBMC = PBMC %>%
# select(1:11, -old.ident) %>%
# mutate(sample = sprintf("./data/seurat/outs/%s", sample)) %>%
# mutate(Phase = sprintf("phase_%s", Phase))
PBMC <- readRDS("dev/PBMC.rds")
PBMC_clean_scaled <-
PBMC_
mutate(grouping = sample) %>%
nest(sample_df = -grouping) %>%
mutate(sample_df = map( sample_df,~ SCTransform(.x)))
my_features =
PBMC_clean_scaled$sample_df %>%
SelectIntegrationFeatures(nfeatures = 2000)
PBMC_integrated =
PBMC_clean_scaled$sample_df %>%
PrepSCTIntegration(anchor.features = my_features) %>%
FindIntegrationAnchors(
normalization.method = "SCT",
anchor.features = my_features
) %>%
IntegrateData(normalization.method = "SCT")
PBMC_integrated %>% saveRDS("dev/PBMC_integrated.rds")
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