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05d_lymphoma_umap.R
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05d_lymphoma_umap.R
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################################################################################
################################################################################
################################################################################
################################################################################
################################ LYMPHOMA UMAP #################################
#################################### SETUP #####################################
library(knitr)
library(tidyverse)
library(matrixStats)
library(data.table)
library(PCAtools)
library(DESeq2)
library(ggplot2)
library(ggsci)
library(edgeR)
library(ashr)
library(cowplot)
library(wesanderson)
library(umap)
library(magrittr)
################################### LOAD DATA ##################################
load("r_outputs/05b-all_lymphoma_pca_dds.Rdata")
load("r_outputs/01-metadata.Rdata")
all_metadata$sample <- row.names(all_metadata)
all_metadata$subtype2 <- all_metadata$subtype
all_metadata$subtype2[all_metadata$cancer_type == "DLBCL"] <-
DLBCL_metadata$LymphGen_call[match(all_metadata$sample, DLBCL_metadata$case)]
all_metadata$subtype2[all_metadata$cancer_type == "BL"] <-
all_metadata$subtype[all_metadata$cancer_type == "BL"]
all_metadata$subtype2[all_metadata$cancer_type == "FL"] <-
all_metadata$subtype[all_metadata$cancer_type == "FL"]
all_metadata$subtype2[is.na(all_metadata$subtype2)] <- "Unknown"
norm.counts.all <- assay(all.tform) %>%
t()
# Perform UMAP on the normalized data
custom <- umap::umap.defaults
custom$n_neighbors <- 9
custom$min_dist <- 0.01
umap.all <-
umap::umap(norm.counts.all, custom)
umap.plot.all.df <-
data.frame(umap.all$layout) %>%
# Turn sample IDs stored as row names into a column
tibble::rownames_to_column("sample") %>%
# Add the metadata into this data frame; match by sample IDs
dplyr::inner_join(all_metadata, by = "sample")
ggplot(
umap.plot.all.df,
aes(
x = X1,
y = X2,
color = subtype,
shape = cancer_type)) +
geom_point() +
theme_cowplot()