Module Sample Contribution Spleen
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.spleen <- log.tdata.FPKM.sample.info.subset %>% rownames_to_column() %>% filter(Tissue == "Spleen") %>% column_to_rownames()
modules <- read.csv(here("Data","Spleen","log.tdata.FPKM.sample.info.subset.spleen.WGCNA.module.membership.csv"), header=T)
eigens <- read.csv(here("Data","Spleen","log.tdata.FPKM.sample.info.subset.spleen.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.spleen)palevioletred3 Module
moccasin Module
grey Module
mediumpurple1 Module
indianred4 Module
slateblue1 Module
coral2 Module
blue3 Module
blue2 Module
black Module
orangered4 Module
tan4 Module
orange Module
thistle1 Module
brown4 Module
darkgreen Module
darkseagreen4 Module
mediumorchid Module
plum Module
thistle3 Module
darkseagreen3 Module
navajowhite Module
sienna2 Module
lightskyblue4 Module
mediumpurple Module
indianred2 Module
royalblue3 Module
cornflowerblue Module
pink2 Module
indianred1 Module
lightblue2 Module
Module Sample Contribution Dot plot
dot.plot(eigens)palevioletred3 Module
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moccasin Module
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grey Module
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mediumpurple1 Module
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indianred4 Module
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slateblue1 Module
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coral2 Module
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blue3 Module
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blue2 Module
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black Module
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orangered4 Module
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tan4 Module
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orange Module
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thistle1 Module
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brown4 Module
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darkgreen Module
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darkseagreen4 Module
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mediumorchid Module
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plum Module
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thistle3 Module
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darkseagreen3 Module
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navajowhite Module
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sienna2 Module
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lightskyblue4 Module
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mediumpurple Module
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indianred2 Module
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royalblue3 Module
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cornflowerblue Module
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pink2 Module
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indianred1 Module
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lightblue2 Module
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Analysis performed by Ann Wells
The Carter Lab The Jackson Laboratory 2023
ann.wells@jax.org