Module Sample Contribution Prefontal Cortex
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.prefrontal.cortex <- log.tdata.FPKM.sample.info.subset %>% rownames_to_column() %>% filter(Tissue == "Pre-frontal Cortex") %>% column_to_rownames()
modules <- read.csv(here("Data","Prefrontal Cortex","log.tdata.FPKM.sample.info.subset.prefrontal.cortex.WGCNA.module.membership.csv"), header=T)
eigens <- read.csv(here("Data","Prefrontal Cortex","log.tdata.FPKM.sample.info.subset.prefrontal.cortex.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.prefrontal.cortex)blanchedalmond Module
chocolate4 Module
black Module
lightgoldenrod3 Module
darkolivegreen2 Module
aquamarine Module
bisque2 Module
darkolivegreen4 Module
grey Module
blueviolet Module
darkturquoise Module
khaki3 Module
dodgerblue4 Module
cornsilk2 Module
darkseagreen4 Module
lightpink1 Module
navajowhite3 Module
antiquewhite Module
pink Module
salmon Module
lavenderblush2 Module
plum Module
goldenrod3 Module
chocolate2 Module
blue4 Module
mistyrose Module
cornsilk Module
lightskyblue2 Module
burlywood Module
oldlace Module
lightblue Module
limegreen Module
hotpink3 Module
lightskyblue Module
mediumorchid1 Module
rosybrown2 Module
Module Sample Contribution Dot plot
dot.plot(eigens)blanchedalmond Module
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chocolate4 Module
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black Module
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lightgoldenrod3 Module
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darkolivegreen2 Module
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aquamarine Module
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bisque2 Module
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darkolivegreen4 Module
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grey Module
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blueviolet Module
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darkturquoise Module
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khaki3 Module
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dodgerblue4 Module
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cornsilk2 Module
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darkseagreen4 Module
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lightpink1 Module
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navajowhite3 Module
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antiquewhite Module
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pink Module
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salmon Module
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lavenderblush2 Module
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plum Module
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goldenrod3 Module
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chocolate2 Module
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blue4 Module
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mistyrose Module
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cornsilk Module
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lightskyblue2 Module
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burlywood Module
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oldlace Module
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lightblue Module
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limegreen Module
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hotpink3 Module
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lightskyblue Module
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mediumorchid1 Module
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rosybrown2 Module
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Analysis performed by Ann Wells
The Carter Lab The Jackson Laboratory 2023
ann.wells@jax.org