Module Sample Contribution Kidney
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.kidney <- log.tdata.FPKM.sample.info.subset %>% rownames_to_column() %>% filter(Tissue == "Kidney") %>% column_to_rownames()
modules <- read.csv(here("Data","Kidney","log.tdata.FPKM.sample.info.subset.kidney.WGCNA.module.membership.csv"), header=T)
eigens <- read.csv(here("Data","Kidney","log.tdata.FPKM.sample.info.subset.kidney.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.kidney)cyan Module
blue Module
red Module
pink Module
magenta Module
darkred Module
midnightblue Module
purple Module
greenyellow Module
salmon Module
lightcyan Module
grey60 Module
lightgreen Module
lightyellow Module
darkgreen Module
darkturquoise Module
darkgrey Module
Module Sample Contribution Dot plot
dot.plot(eigens)cyan Module
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blue Module
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red Module
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pink Module
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magenta Module
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darkred Module
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midnightblue Module
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purple Module
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greenyellow Module
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salmon Module
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lightcyan Module
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grey60 Module
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lightgreen Module
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lightyellow Module
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darkgreen Module
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darkturquoise Module
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darkgrey Module
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Analysis performed by Ann Wells
The Carter Lab The Jackson Laboratory 2023
ann.wells@jax.org