Module Sample Contribution Brain
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.hip.hyp.cortex <- log.tdata.FPKM.sample.info.subset %>% rownames_to_column() %>% filter(Tissue %in% c("Hippocampus", "Hypothanamus","Pre-frontal Cortex")) %>% column_to_rownames()
#log.tdata.FPKM.sample.info.subset.hip.hyp.cortex$Treatment[log.tdata.FPKM.sample.info.subset.hip.hyp.cortex$Treatment=="None"] <- "Control"
modules <- read.csv(here("Data","Brain","log.tdata.FPKM.sample.info.subset.hip.hyp.cortex.WGCNA.module.membership.csv"), header=T)
eigens <- read.csv(here("Data","Brain","log.tdata.FPKM.sample.info.subset.hip.hyp.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.hip.hyp.cortex)antiquewhite Module
cyan Module
lavenderblush1 Module
darkolivegreen4 Module
darkgrey Module
brown3 Module
orangered1 Module
deeppink2 Module
grey Module
magenta1 Module
mediumpurple Module
darkslateblue Module
magenta4 Module
firebrick4 Module
honeydew Module
brown1 Module
coral3 Module
royalblue Module
green3 Module
lavenderblush3 Module
green4 Module
lightblue1 Module
magenta3 Module
blanchedalmond Module
orangered4 Module
darkseagreen Module
paleturquoise4 Module
chocolate3 Module
indianred3 Module
plum Module
lightcoral Module
aliceblue Module
burlywood Module
thistle3 Module
lavenderblush2 Module
pink2 Module
lightblue2 Module
wheat3 Module
mediumorchid3 Module
orange3 Module
dodgerblue4 Module
Module Sample Contribution Dot plot
dot.plot(eigens)antiquewhite Module
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cyan Module
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lavenderblush1 Module
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darkolivegreen4 Module
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darkgrey Module
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brown3 Module
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orangered1 Module
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deeppink2 Module
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grey Module
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magenta1 Module
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mediumpurple Module
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darkslateblue Module
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magenta4 Module
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firebrick4 Module
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honeydew Module
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brown1 Module
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coral3 Module
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royalblue Module
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green3 Module
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lavenderblush3 Module
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green4 Module
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lightblue1 Module
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magenta3 Module
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blanchedalmond Module
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orangered4 Module
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darkseagreen Module
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paleturquoise4 Module
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chocolate3 Module
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indianred3 Module
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plum Module
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lightcoral Module
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aliceblue Module
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burlywood Module
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thistle3 Module
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lavenderblush2 Module
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pink2 Module
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lightblue2 Module
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wheat3 Module
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mediumorchid3 Module
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orange3 Module
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dodgerblue4 Module
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Analysis performed by Ann Wells
The Carter Lab The Jackson Laboratory 2023
ann.wells@jax.org