Module Sample Contribution Hypothalamus
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 (add dosage) 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.hypothalamus <- log.tdata.FPKM.sample.info.subset %>% rownames_to_column() %>% filter(Tissue == "Hypothanamus") %>% column_to_rownames()
log.tdata.FPKM.sample.info.subset.hypothalamus$Tissue <- gsub("Hypothanamus","Hypothalamus",log.tdata.FPKM.sample.info.subset.hypothalamus$Tissue)
modules <- read.csv(here("Data","Hypothalamus","log.tdata.FPKM.sample.info.subset.hypothalamus.WGCNA.module.membership.csv"), header=T)
eigens <- read.csv(here("Data","Hypothalamus","log.tdata.FPKM.sample.info.subset.hypothalamus.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.hypothalamus)black Module
indianred4 Module
lightgreen Module
antiquewhite2 Module
blue Module
antiquewhite4 Module
lightblue4 Module
darkgreen Module
brown2 Module
bisque4 Module
darkturquoise Module
lightpink4 Module
midnightblue Module
thistle3 Module
skyblue Module
lightsteelblue1 Module
darkslateblue Module
grey Module
salmon4 Module
navajowhite2 Module
plum Module
lavenderblush2 Module
orangered1 Module
mediumpurple1 Module
lightslateblue Module
Module Sample Contribution Dot plot
dot.plot(eigens)black Module
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indianred4 Module
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lightgreen Module
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antiquewhite2 Module
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blue Module
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antiquewhite4 Module
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lightblue4 Module
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darkgreen Module
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brown2 Module
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bisque4 Module
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darkturquoise Module
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lightpink4 Module
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midnightblue Module
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thistle3 Module
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skyblue Module
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lightsteelblue1 Module
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darkslateblue Module
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grey Module
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salmon4 Module
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navajowhite2 Module
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plum Module
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lavenderblush2 Module
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orangered1 Module
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mediumpurple1 Module
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lightslateblue Module
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Analysis performed by Ann Wells
The Carter Lab The Jackson Laboratory 2023
ann.wells@jax.org