Contribution of Main Effects Prefrontal Cortex
Ann Wells
April 23, 2023
Introduction and Data files
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 the contribution of each main effect or their combination to each module identified, as well as the relationship of each gene within the module and its significance.
needed.packages <- c("tidyverse", "here", "functional", "gplots", "dplyr", "GeneOverlap", "R.utils", "reshape2","magrittr","data.table", "RColorBrewer","preprocessCore", "ARTool","emmeans", "phia", "gProfileR", "WGCNA","plotly", "pheatmap","ppcor", "pander","downloadthis")
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","WGCNA_contribution_source.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.subset <- log.tdata.FPKM.subset %>% rownames_to_column() %>% filter(rowname != "A113") %>% column_to_rownames()
log.tdata.FPKM.sample.info.subset.prefrontal.cortex <- log.tdata.FPKM.sample.info %>% rownames_to_column() %>% filter(Tissue == "Pre-frontal Cortex") %>% column_to_rownames()
log.tdata.FPKM.subset <- subset(log.tdata.FPKM.sample.info.subset.prefrontal.cortex, select = -c(Time,Treatment,Tissue))
WGCNA.pathway <-readRDS(here("Data","Prefrontal Cortex","Chang_B6_96hr_4wk_gprofiler_pathway_annotation_list_prefrontal_cortex_WGCNA.RData"))
Matched<-readRDS(here("Data","Prefrontal Cortex","Annotated_genes_in_prefrontal_cortex_WGCNA_Chang_B6_96hr_4wk.RData"))
module.names <- Matched$X..Module.
name <- str_split(module.names,"_")
samples <-c()
for(i in 1:length(name)){
samples[[i]] <- name[[i]][2]
}
name <- str_split(samples,"\"")
name <- unlist(name)
Treatment <- unclass(as.factor(log.tdata.FPKM.sample.info.subset.prefrontal.cortex[,27238]))
Time <- unclass(as.factor(log.tdata.FPKM.sample.info.subset.prefrontal.cortex[,27237]))
Treat.Time <- paste0(Treatment, Time)
phenotype <- data.frame(cbind(Treatment, Time, Treat.Time))
nSamples <- nrow(log.tdata.FPKM.sample.info.subset.prefrontal.cortex)
MEs0 <- read.csv(here("Data","Prefrontal Cortex","log.tdata.FPKM.sample.info.subset.prefrontal.cortex.WGCNA.module.eigens.csv"),header = T, row.names = 1)
name <- str_split(names(MEs0),"_")
samples <-c()
for(i in 1:length(name)){
samples[[i]] <- name[[i]][2]
}
name <- str_split(samples,"\"")
name <- unlist(name)
colnames(MEs0) <-name
MEs <- orderMEs(MEs0)
moduleTraitCor <- cor(MEs, phenotype, use = "p");
moduleTraitPvalue <- corPvalueStudent(moduleTraitCor, nSamples)Relationship between Modules and Traits
#sizeGrWindow(10,6)
# Will display correlations and their p-values
textMatrix = paste(signif(moduleTraitCor, 2), "\n(",
signif(moduleTraitPvalue, 1), ")", sep = "");
dim(textMatrix) = dim(moduleTraitCor)
# Display the correlation values within a heatmap plot
heat <- pheatmap(moduleTraitCor, main = paste("Module-trait relationships"), color=colorRampPalette(brewer.pal(n = 12, name = "Paired"))(10), cluster_rows = F, cluster_cols = F, fontsize_number = 4, angle_col = 45, number_color = "black", border_color = "white")
heat
DT::datatable(moduleTraitPvalue, extensions = 'Buttons',
rownames = TRUE,
filter="top",
options = list(dom = 'Blfrtip',
buttons = c('copy', 'csv', 'excel'),
lengthMenu = list(c(10,25,50,-1),
c(10,25,50,"All")),
scrollX= TRUE), class = "display")Partial Correlation
phenotype$Treatment <- as.numeric(phenotype$Treatment)
phenotype$Time <- as.numeric(phenotype$Time)
phenotype$Treat.Time <- as.numeric(phenotype$Treat.Time)
Sigmodules <- as.data.frame(cbind(MEs$limegreen,MEs$rosybrown2, MEs$lavenderblush2,MEs$antiquewhite,MEs$pink,MEs$lightpink1,MEs$goldenrod3,MEs$aquamarine,MEs$mistyrose))
colnames(Sigmodules) <- c("limegreen","rosybrown2","lavenderblush2","antiquewhite","pink","lightpink1","goldenrod3","aquamarine","mistyrose")
for(i in 1:length(Sigmodules)){
cat("\n##",colnames(Sigmodules[i]),"{.tabset .tabset-fade .tabset-pills}","\n")
for(j in 1:length(phenotype)){
cat("\n###", colnames(phenotype[j]),"{.tabset .tabset-fade .tabset-pills}","\n")
for(k in 1:length(phenotype)){
cat("\n####", "Partial Correlation", colnames(phenotype[k]),"\n")
partial <- pcor.test(Sigmodules[,i], phenotype[,j],phenotype[,k])
panderOptions('knitr.auto.asis', FALSE)
print(pander(partial))
cat("\n \n")
}
cat("\n \n")
}
cat("\n \n")
}limegreen
Treatment
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4881 | 0.06493 | 2.016 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.505 | 0.05486 | 2.11 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.3424 | 0.2115 | 1.314 | 16 | 1 | pearson |
NULL
Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.2942 | 0.2872 | -1.11 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.2567 | 0.3556 | -0.9578 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.3424 | 0.2115 | -1.314 | 16 | 1 | pearson |
NULL
Treat.Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.2942 | 0.2872 | -1.11 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.505 | 0.05486 | 2.11 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4601 | 0.08441 | 1.868 | 16 | 1 | pearson |
NULL
rosybrown2
Treatment
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.5122 | 0.05092 | 2.15 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.5517 | 0.03298 | 2.385 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4775 | 0.07188 | 1.959 | 16 | 1 | pearson |
NULL
Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.4327 | 0.1072 | -1.731 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.3716 | 0.1726 | -1.443 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.4775 | 0.07188 | -1.959 | 16 | 1 | pearson |
NULL
Treat.Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.4327 | 0.1072 | -1.731 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.5517 | 0.03298 | 2.385 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4727 | 0.07517 | 1.934 | 16 | 1 | pearson |
NULL
lavenderblush2
Treatment
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4508 | 0.09169 | 1.821 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4529 | 0.09004 | 1.831 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.05596 | 0.843 | -0.2021 | 16 | 1 | pearson |
NULL
Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.1065 | 0.7056 | 0.3862 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.09507 | 0.7361 | 0.3443 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.05596 | 0.843 | 0.2021 | 16 | 1 | pearson |
NULL
Treat.Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.1065 | 0.7056 | 0.3862 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4529 | 0.09004 | 1.831 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.458 | 0.08598 | 1.858 | 16 | 1 | pearson |
NULL
antiquewhite
Treatment
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.7385 | 0.001666 | -3.949 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.7386 | 0.001662 | -3.95 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.08269 | 0.7696 | -0.2992 | 16 | 1 | pearson |
NULL
Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.02616 | 0.9263 | -0.09435 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.01764 | 0.9502 | -0.06361 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.08269 | 0.7696 | 0.2992 | 16 | 1 | pearson |
NULL
Treat.Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.02616 | 0.9263 | -0.09435 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.7386 | 0.001662 | -3.95 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.7366 | 0.001738 | -3.926 | 16 | 1 | pearson |
NULL
pink
Treatment
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.8591 | 4.087e-05 | -6.052 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.9057 | 3.377e-06 | -7.703 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.7057 | 0.003286 | -3.591 | 16 | 1 | pearson |
NULL
Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.6186 | 0.01395 | 2.839 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.3166 | 0.2502 | 1.204 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.7057 | 0.003286 | 3.591 | 16 | 1 | pearson |
NULL
Treat.Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.6186 | 0.01395 | 2.839 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.9057 | 3.377e-06 | -7.703 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.8233 | 0.0001624 | -5.23 | 16 | 1 | pearson |
NULL
lightpink1
Treatment
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.3816 | 0.1605 | -1.488 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.4564 | 0.08722 | -1.85 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.6176 | 0.01416 | -2.831 | 16 | 1 | pearson |
NULL
Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.5937 | 0.01962 | 2.66 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.5488 | 0.03412 | 2.367 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.6176 | 0.01416 | 2.831 | 16 | 1 | pearson |
NULL
Treat.Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.5937 | 0.01962 | 2.66 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.4564 | 0.08722 | -1.85 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.3251 | 0.2371 | -1.239 | 16 | 1 | pearson |
NULL
goldenrod3
Treatment
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.08907 | 0.7523 | 0.3224 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.1018 | 0.7181 | 0.369 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.4776 | 0.07181 | -1.96 | 16 | 1 | pearson |
NULL
Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4863 | 0.06606 | 2.007 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4843 | 0.06731 | 1.996 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4776 | 0.07181 | 1.96 | 16 | 1 | pearson |
NULL
Treat.Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4863 | 0.06606 | 2.007 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.1018 | 0.7181 | 0.369 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.1368 | 0.6268 | 0.498 | 16 | 1 | pearson |
NULL
aquamarine
Treatment
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.443 | 0.09817 | -1.782 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.4934 | 0.06162 | -2.045 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.5254 | 0.0443 | -2.226 | 16 | 1 | pearson |
NULL
Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4911 | 0.06301 | 2.033 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4403 | 0.1005 | 1.768 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.5254 | 0.0443 | 2.226 | 16 | 1 | pearson |
NULL
Treat.Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4911 | 0.06301 | 2.033 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.4934 | 0.06162 | -2.045 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.397 | 0.1429 | -1.56 | 16 | 1 | pearson |
NULL
mistyrose
Treatment
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.3937 | 0.1465 | 1.544 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4098 | 0.1293 | 1.62 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| -0.2604 | 0.3486 | -0.9725 | 16 | 1 | pearson |
NULL
Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.3013 | 0.2751 | 1.139 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.277 | 0.3176 | 1.039 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.2604 | 0.3486 | 0.9725 | 16 | 1 | pearson |
NULL
Treat.Time
Partial Correlation Treatment
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.3013 | 0.2751 | 1.139 | 16 | 1 | pearson |
NULL
Partial Correlation Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4098 | 0.1293 | 1.62 | 16 | 1 | pearson |
NULL
Partial Correlation Treat.Time
| estimate | p.value | statistic | n | gp | Method |
|---|---|---|---|---|---|
| 0.4193 | 0.1197 | 1.665 | 16 | 1 | pearson |
NULL
Scatterplots Module membership vs. Gene significance
Time
time.contribution(phenotype, log.tdata.FPKM.subset, MEs)grey
limegreen
black
darkturquoise
mistyrose
lightpink1
goldenrod3
lightblue
darkolivegreen2
dodgerblue4
chocolate4
rosybrown2
lightgoldenrod3
khaki3
salmon
lavenderblush2
burlywood
mediumorchid1
blueviolet
plum
lightskyblue2
antiquewhite
chocolate2
darkseagreen4
hotpink3
bisque2
cornsilk2
cornsilk
oldlace
lightskyblue
darkolivegreen4
blanchedalmond
aquamarine
pink
blue4
Treatment
treat.contribution(phenotype, log.tdata.FPKM.subset, MEs)grey
limegreen
black
darkturquoise
mistyrose
lightpink1
goldenrod3
lightblue
darkolivegreen2
dodgerblue4
chocolate4
rosybrown2
lightgoldenrod3
khaki3
salmon
lavenderblush2
burlywood
mediumorchid1
blueviolet
plum
lightskyblue2
antiquewhite
chocolate2
darkseagreen4
hotpink3
bisque2
cornsilk2
cornsilk
oldlace
lightskyblue
darkolivegreen4
blanchedalmond
aquamarine
pink
blue4
Treatment by Time
treat.time.contribution(phenotype, log.tdata.FPKM.subset, MEs)grey
limegreen
black
darkturquoise
mistyrose
lightpink1
goldenrod3
lightblue
darkolivegreen2
dodgerblue4
chocolate4
rosybrown2
lightgoldenrod3
khaki3
salmon
lavenderblush2
burlywood
mediumorchid1
blueviolet
plum
lightskyblue2
antiquewhite
chocolate2
darkseagreen4
hotpink3
bisque2
cornsilk2
cornsilk
oldlace
lightskyblue
darkolivegreen4
blanchedalmond
aquamarine
pink
blue4
Analysis performed by Ann Wells
The Carter Lab The Jackson Laboratory 2023
ann.wells@jax.org