Module Sample Contribution Hippocampus
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.hippocampus <- log.tdata.FPKM.sample.info.subset %>% rownames_to_column() %>% filter(Tissue == "Hippocampus") %>% column_to_rownames()
modules <- read.csv(here("Data","Hippocampus","log.tdata.FPKM.sample.info.subset.hippocampus.WGCNA.module.membership.csv"), header=T)
eigens <- read.csv(here("Data","Hippocampus","log.tdata.FPKM.sample.info.subset.hippocampus.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.hippocampus)goldenrod4 Module
brown2 Module
deepskyblue4 Module
coral1 Module
turquoise Module
darkseagreen2 Module
chocolate3 Module
darkgrey Module
brown1 Module
pink1 Module
indianred1 Module
tan4 Module
dodgerblue1 Module
green Module
darkslateblue Module
grey Module
lavenderblush2 Module
indianred4 Module
tomato Module
pink4 Module
slateblue1 Module
blue3 Module
blanchedalmond Module
darkolivegreen Module
green3 Module
dodgerblue3 Module
chocolate2 Module
lavenderblush3 Module
chocolate Module
orangered1 Module
firebrick3 Module
deeppink Module
salmon1 Module
lavenderblush1 Module
firebrick2 Module
indianred2 Module
blue1 Module
darkgoldenrod4 Module
antiquewhite Module
orange3 Module
tan1 Module
darkgoldenrod1 Module
rosybrown3 Module
khaki3 Module
bisque2 Module
Module Sample Contribution Dot plot
dot.plot(eigens)goldenrod4 Module
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brown2 Module
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deepskyblue4 Module
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coral1 Module
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turquoise Module
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darkseagreen2 Module
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chocolate3 Module
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darkgrey Module
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brown1 Module
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pink1 Module
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indianred1 Module
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tan4 Module
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dodgerblue1 Module
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green Module
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darkslateblue Module
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grey Module
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lavenderblush2 Module
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indianred4 Module
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tomato Module
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pink4 Module
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slateblue1 Module
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blue3 Module
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blanchedalmond Module
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darkolivegreen Module
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green3 Module
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dodgerblue3 Module
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chocolate2 Module
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lavenderblush3 Module
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chocolate Module
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orangered1 Module
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firebrick3 Module
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deeppink Module
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salmon1 Module
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lavenderblush1 Module
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firebrick2 Module
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indianred2 Module
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blue1 Module
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darkgoldenrod4 Module
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antiquewhite Module
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orange3 Module
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tan1 Module
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darkgoldenrod1 Module
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rosybrown3 Module
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khaki3 Module
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bisque2 Module
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Analysis performed by Ann Wells
The Carter Lab The Jackson Laboratory 2023
ann.wells@jax.org