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massqc_qc_correlation.Rmd
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massqc_qc_correlation.Rmd
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---
title: "QC sample correlation plot"
author:
- name: Xiaotao Shen (https://www.shenxt.info/)
date: "Created on 2021-12-04 and updated on `r Sys.Date()`"
output:
html_document:
df_print: paged
toc: no
pdf_document:
toc: no
vignette: >
%\VignetteIndexEntry{qc_correlation}
%\VignettePackage{massqc}
% \VignetteEngine{knitr::rmarkdown}
% \usepackage[utf8]{inputenc}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE, echo=FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
warning = FALSE,
message = TRUE,
out.width = "100%"
)
```
# **Data preparation**
```{r,eval=TRUE,warning=FALSE, R.options="", message=FALSE, cache=TRUE}
library(massdataset)
library(tidyverse)
library(massqc)
data("sample_info", package = "massdataset")
data("expression_data", package = "massdataset")
data("variable_info", package = "massdataset")
object =
create_mass_dataset(
expression_data = expression_data,
sample_info = sample_info,
variable_info = variable_info
)
object
```
# **QC correlation plot**
```{r,eval=TRUE,warning=FALSE, R.options="", message=FALSE, cache=TRUE}
object %>%
massqc_sample_correlation()
object %>%
massqc_sample_correlation()
object %>%
activate_mass_dataset(what = "sample_info") %>%
filter(class == "QC") %>%
massqc_sample_correlation()
object %>%
massqc_sample_correlation(lab = TRUE)
object %>%
massqc_sample_correlation(lab = TRUE, type = "upper")
```
# **Session information**
```{r,eval=TRUE,warning=FALSE, R.options="", message=FALSE, cache=TRUE}
sessionInfo()
```