In shbrief/GenomicSuperSignaturePaper: Reproduce GenomicSuperSignature paper

knitr::opts_chunk$set(
  comment = "#>", collapse = TRUE, message = FALSE, warning = FALSE,
  out.height="50%", out.width="50%"
)

if (!"pathwork" %in% installed.packages())
    devtools::install_github("thomasp85/patchwork")

suppressPackageStartupMessages({
  library(patchwork)
  library(pdftools)
})

knitr::include_graphics("others/available_samples.png")

Benchmark CRC paper

CRC_top10_validated_ind.tsv

A data frame of top 10 validated indexes from 18 CRC datasets. This table was created in CRC/repeat_Fig4A.Rmd

x <- read.table("CRC/outputs/CRC_top10_validated_ind.tsv")
head(x)

CRC subtyping

Scatter plots showing how different signatures perform with CRC subtyping. These plots were created in CRC/repeat_Fig4A.Rmd

all <- list.files("CRC/outputs")
scatterplots <- all[grep("scatter_.*rds", all)]

for (plot in scatterplots) {
  x <- readRDS(file.path("CRC/outputs", plot))
  print(x)
}

CRC binary clinical variables

Bar plots comparing different models in differentiating CRC binary clinical variables. These plots were created in CRC/repeat_Fig4C.Rmd

all <- list.files("CRC/outputs")
barplots <- all[grep("boxplot_.*rds", all)]

for (plot in barplots) {
  x <- readRDS(file.path("CRC/outputs", plot))
  print(x$value)
}

Benchmark multiPLIER

neutrophil_estimate.rds

Two scatter plots of RAV1551 x Neutrophil count/estimate of SLE-WB dataset. This plot was created in SLE-WB/repeat_Fig3_SLE-WB.Rmd

x <- readRDS("SLE-WB/outputs/neutrophil_estimate.rds")
x

nares_neutrophil.rds

A scatter plot of RAV1551 x Neutrophil estimate of NARES dataset. This plot was created in NARES/repeat_Fig3_NARES.Rmd

x <- readRDS("NARES/outputs/nares_neutrophil.rds")
x

Session Info

sessionInfo()

shbrief/GenomicSuperSignaturePaper documentation built on Aug. 2, 2022, 2:04 p.m.