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2023-08-29_sl.Rmd
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2023-08-29_sl.Rmd
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---
title: "2023-08-29_sl"
author: "kim soyeon"
date: "2023-08-29"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(phyloseq)
library(microbiomeMarker)
library(ggplot2)
library(dplyr)
ps <- readRDS("./ps.rds") %>%
subset_samples(body.site %in% c("gut", "tongue"))
ps
```
# supervised leaning (SL) methods
## random forest
```{r}
LR.1 <- microbiomeMarker::run_sl(
ps = ps,
group = "body.site",
method = "LR")
microbiomeMarker::plot_sl_roc(LR.1, group = "body.site")
ggsave("./Marker_LR01_roc.png")
microbiomeMarker::plot_ef_bar(LR.1)
ggsave("./Marker_LR01_bar.png")
LR.2 <- microbiomeMarker::run_sl(
ps = ps,
norm = "TSS",
group = "body.site",
method = "LR",
taxa_rank = "Genus")
microbiomeMarker::plot_sl_roc(LR.2, group = "body.site")
ggsave("./Marker_LR02_roc.png")
microbiomeMarker::plot_ef_bar(LR.2)
ggsave("./Marker_LR02_bar.png")
```
## SVM
```{r}
SVM.1 <- microbiomeMarker::run_sl(
ps = ps,
group = "body.site",
method = "SVM")
microbiomeMarker::plot_sl_roc(SVM.1, group = "body.site")
ggsave("./Marker_SVM01_roc.png")
microbiomeMarker::plot_ef_bar(SVM.1)
ggsave("./Marker_SVM01_bar.png")
SVM.2 <- microbiomeMarker::run_sl(
ps = ps,
norm = "CLR",
group = "body.site",
method = "SVM",
taxa_rank = "Species",
nfolds = 2,
nrepeats = 1,
top_n = 10)
microbiomeMarker::plot_sl_roc(SVM.2, group = "body.site")
ggsave("./Marker_SVM02_roc.png")
microbiomeMarker::plot_ef_bar(SVM.2)
ggsave("./Marker_SVM02_bar.png")
microbiomeMarker::plot_cladogram(SVM.2, color = c("darkgreen", "red"))
ggsave("./Marker_SVM02_cla.png")
?plot_cladogram
```
## random forest
```{r}
Rf.1 <- microbiomeMarker::run_sl(
ps = ps,
group = "body.site",
method = "RF")
?run_sl
microbiomeMarker::plot_sl_roc(Rf.1, group = "subject")
microbiomeMarker::plot_ef_bar(Rf.1)
```
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