Module Sample Contribution Liver
Ann Wells
April 23, 2023
Introduction and Data files
R Markdown
This dataset contains nine tissues (heart, hippocampus, hypothalamus, kidney, liver, prefrontal cortex, skeletal muscle, small intestine, and spleen) from C57BL/6J mice that were fed 2-deoxyglucose (6g/L) through their drinking water for 96hrs or 4wks. 96hr mice were given their 2DG treatment 2 weeks after the other cohort started the 4 week treatment. The organs from the mice were harvested and processed for metabolomics and transcriptomics. The data in this document pertains to the transcriptomics data only. The counts that were used were FPKM normalized before being log transformed. It was determined that sample A113 had low RNAseq quality and through further analyses with PCA, MA plots, and clustering was an outlier and will be removed for the rest of the analyses performed. This document will determine how samples are contributing to each module.
needed.packages <- c("tidyverse", "here", "functional", "gplots", "dplyr", "GeneOverlap", "R.utils", "reshape2","magrittr","data.table", "RColorBrewer","preprocessCore", "ARTool","emmeans", "phia", "gProfileR","pheatmap")
for(i in 1:length(needed.packages)){library(needed.packages[i], character.only = TRUE)}
source(here("source_files","WGCNA_source.R"))
source(here("source_files","plot_theme.R"))tdata.FPKM.sample.info <- readRDS(here("Data","20190406_RNAseq_B6_4wk_2DG_counts_phenotypes.RData"))
tdata.FPKM <- readRDS(here("Data","20190406_RNAseq_B6_4wk_2DG_counts_numeric.RData"))
log.tdata.FPKM <- log(tdata.FPKM + 1)
log.tdata.FPKM <- as.data.frame(log.tdata.FPKM)
log.tdata.FPKM.sample.info <- cbind(log.tdata.FPKM, tdata.FPKM.sample.info[,27238:27240])
log.tdata.FPKM.sample.info <- log.tdata.FPKM.sample.info %>% rownames_to_column() %>% filter(rowname != "A113") %>% column_to_rownames()
log.tdata.FPKM.subset <- log.tdata.FPKM[,colMeans(log.tdata.FPKM != 0) > 0.5]
log.tdata.FPKM.sample.info.subset <- cbind(log.tdata.FPKM.subset,tdata.FPKM.sample.info[,27238:27240])
log.tdata.FPKM.sample.info.subset <- log.tdata.FPKM.sample.info.subset %>% rownames_to_column() %>% filter(rowname != "A113") %>% column_to_rownames()
log.tdata.FPKM.sample.info.subset.liver <- log.tdata.FPKM.sample.info.subset %>% rownames_to_column() %>% filter(Tissue == "Liver") %>% column_to_rownames()
modules <- read.csv(here("Data","Liver","log.tdata.FPKM.sample.info.subset.liver.WGCNA.module.membership.csv"), header=T)
eigens <- read.csv(here("Data","Liver","log.tdata.FPKM.sample.info.subset.liver.WGCNA.module.eigens.csv"), header=T)Module Sample Contribution
The heatmap shows the expression level of each gene in the module across all samples present in this subsetted dataset. The bar plot shows the relative eigen value summarizing gene expression for each sample present in this subsetted dataset.
eigen.expression(eigens,log.tdata.FPKM.sample.info.subset.liver)turquoise Module
darkgrey Module
grey60 Module
brown Module
salmon Module
cyan Module
green Module
black Module
pink Module
darkolivegreen Module
tan Module
lightcyan Module
plum2 Module
lightgreen Module
darkorange Module
darkred Module
darkgreen Module
darkturquoise Module
orange Module
skyblue Module
violet Module
yellowgreen Module
skyblue3 Module
mediumpurple3 Module
lightsteelblue1 Module
lightcyan1 Module
darkorange2 Module
ivory Module
brown4 Module
bisque4 Module
darkslateblue Module
Module Sample Contribution Dot plot
dot.plot(eigens)turquoise Module
Time
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darkgrey Module
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grey60 Module
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brown Module
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salmon Module
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cyan Module
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green Module
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black Module
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pink Module
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darkolivegreen Module
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tan Module
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lightcyan Module
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plum2 Module
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lightgreen Module
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darkorange Module
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darkred Module
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darkgreen Module
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darkturquoise Module
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orange Module
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skyblue Module
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violet Module
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yellowgreen Module
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skyblue3 Module
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mediumpurple3 Module
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lightsteelblue1 Module
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Time_by_Treatment
lightcyan1 Module
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Time_by_Treatment
darkorange2 Module
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Time_by_Treatment
ivory Module
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brown4 Module
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bisque4 Module
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darkslateblue Module
Time
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Time_by_Treatment
Analysis performed by Ann Wells
The Carter Lab The Jackson Laboratory 2023
ann.wells@jax.org