Module Sample Contribution Small Intestine
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.small.intestine <- log.tdata.FPKM.sample.info.subset %>% rownames_to_column() %>% filter(Tissue == "Small Intestine") %>% column_to_rownames()
modules <- read.csv(here("Data","Small Intestine","log.tdata.FPKM.sample.info.subset.small.intestine.WGCNA.module.membership.csv"), header=T)
eigens <- read.csv(here("Data","Small Intestine","log.tdata.FPKM.sample.info.subset.small.intestine.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.small.intestine)cornsilk Module
blue1 Module
rosybrown3 Module
antiquewhite2 Module
aliceblue Module
blue3 Module
coral1 Module
magenta3 Module
burlywood Module
lightblue2 Module
green4 Module
antiquewhite1 Module
sienna3 Module
coral4 Module
blue2 Module
antiquewhite4 Module
firebrick Module
deepskyblue Module
hotpink4 Module
grey Module
lightgreen Module
rosybrown4 Module
royalblue Module
orange Module
white Module
slateblue2 Module
magenta2 Module
mediumpurple3 Module
thistle2 Module
yellow4 Module
indianred Module
antiquewhite Module
mediumpurple1 Module
lightblue4 Module
firebrick3 Module
mistyrose Module
moccasin Module
chocolate3 Module
pink2 Module
sienna1 Module
darkgoldenrod4 Module
lightskyblue2 Module
linen Module
oldlace Module
lightblue Module
red4 Module
Module Sample Contribution Dot plot
dot.plot(eigens)cornsilk Module
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blue1 Module
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rosybrown3 Module
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antiquewhite2 Module
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aliceblue Module
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blue3 Module
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coral1 Module
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magenta3 Module
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burlywood Module
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lightblue2 Module
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green4 Module
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antiquewhite1 Module
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sienna3 Module
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coral4 Module
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blue2 Module
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antiquewhite4 Module
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firebrick Module
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deepskyblue Module
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hotpink4 Module
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grey Module
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lightgreen Module
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rosybrown4 Module
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royalblue Module
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orange Module
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white Module
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slateblue2 Module
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magenta2 Module
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mediumpurple3 Module
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thistle2 Module
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yellow4 Module
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indianred Module
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antiquewhite Module
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mediumpurple1 Module
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lightblue4 Module
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firebrick3 Module
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mistyrose Module
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moccasin Module
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chocolate3 Module
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pink2 Module
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sienna1 Module
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darkgoldenrod4 Module
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lightskyblue2 Module
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linen Module
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oldlace Module
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lightblue Module
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red4 Module
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Analysis performed by Ann Wells
The Carter Lab The Jackson Laboratory 2023
ann.wells@jax.org