Module Sample Contribution Heart
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","colorBlindness")
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.heart <- log.tdata.FPKM.sample.info.subset %>% rownames_to_column() %>% filter(Tissue == "Heart") %>% column_to_rownames()
modules <- read.csv(here("Data","Heart","log.tdata.FPKM.sample.info.subset.heart.WGCNA.module.membership.csv"), header=T)
eigens <- read.csv(here("Data","Heart","log.tdata.FPKM.sample.info.subset.heart.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.heart)plum1 Module
brown Module
darkred Module
cyan Module
black Module
royalblue Module
pink Module
lightgreen Module
darkturquoise Module
lightyellow Module
darkmagenta Module
darkgreen Module
darkgrey Module
darkorange Module
skyblue Module
saddlebrown Module
steelblue Module
paleturquoise Module
violet Module
sienna3 Module
yellowgreen Module
skyblue3 Module
mediumpurple3 Module
lightsteelblue1 Module
lightcyan1 Module
Module Sample Contribution Dot plot
dot.plot(eigens)plum1 Module
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brown Module
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darkred Module
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cyan Module
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black Module
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royalblue Module
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pink Module
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lightgreen Module
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darkturquoise Module
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lightyellow Module
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darkmagenta Module
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darkgreen Module
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darkgrey Module
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darkorange Module
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skyblue Module
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saddlebrown Module
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steelblue Module
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paleturquoise Module
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violet Module
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sienna3 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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lightcyan1 Module
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Analysis performed by Ann Wells
The Carter Lab The Jackson Laboratory 2023
ann.wells@jax.org