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inst/doc/geneplast_Trefflich2019.R
In geneplast: Evolutionary and plasticity analysis of orthologous groups
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
## ----eval=TRUE, message=FALSE, results='hide'---------------------------------
#-- Call packages
library(geneplast)
library(geneplast.data.string.v91)
library(RTN)
library(Fletcher2013b)
library(ggplot2)
library(ggpubr)
library(plyr)
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# #-- Load orthology data from the 'geneplast.data.string.v91' package
# data(gpdata_string_v91)
#
# #-- Create an object of class 'OGR' for a reference 'spid'
# ogr <- groot.preprocess(cogdata=cogdata, phyloTree=phyloTree, spid="9606")
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# #-- Run the 'groot' function and infer the evolutionary roots
# ogr <- groot(ogr, nPermutations=1000, verbose=TRUE)
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# #-- Load regulons
# data("rtni1st")
# tni.regulon.summary(rtni1st)
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# ## This regulatory network comprised of 809 regulons.
# ## -- DPI-filtered network:
# ## regulatoryElements Targets Edges
# ## 809 14131 47012
# ## Min. 1st Qu. Median Mean 3rd Qu. Max.
# ## 0.0 10.0 37.0 58.1 80.0 523.0
# ## -- Reference network:
# ## regulatoryElements Targets Edges
# ## 809 14131 617672
# ## Min. 1st Qu. Median Mean 3rd Qu. Max.
# ## 0 43 449 764 1245 4148
# ## ---
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# #-- Put regulons into an 'igraph' object
# #-- Note: small regulons (n<15 targets) are romeved in this step.
# graph <- tni.graph(rtni1st, gtype = "rmap")
#
# #-- Map the 'ogr' object to the 'igraph' object
# graph <- ogr2igraph(ogr, cogdata, graph, idkey = "ENTREZ")
#
# #-- Make a data frame with the gene roots
# roots_df <- data.frame(COGID = V(graph)$COGID,
# SYMBOL = V(graph)$SYMBOL,
# ENTREZ = V(graph)$ENTREZ,
# Root = V(graph)$Root,
# TRN_element = c("Target","TF")[V(graph)$tfs+1],
# stringsAsFactors = FALSE)
## ----eval=FALSE---------------------------------------------------------------
# #-- Remove NAs from missing annotation
# roots_df <- roots_df[complete.cases(roots_df),]
#
# #-- Remove genes rooted at the base of the phylogenetic tree
# roots_df <- roots_df[roots_df$Root<max(roots_df$Root),]
# rownames(roots_df) <- 1:nrow(roots_df)
#
# #-- Check TF and target counts
# table(roots_df$TRN_element)
## ----eval=FALSE---------------------------------------------------------------
# ## Target TF
# ## 6308 307
## ----eval=FALSE---------------------------------------------------------------
# head(roots_df)
## ----eval=FALSE---------------------------------------------------------------
# ## COGID SYMBOL ENTREZ Root TRN_element
# ## 1 KOG3119 CEBPG 1054 19 TF
# ## 2 KOG4217 NR4A2 4929 17 TF
# ## 3 KOG0493 EN1 2019 17 TF
# ## 4 NOG80479 TP53 7157 20 TF
# ## 5 KOG3740 GATAD2A 54815 19 TF
# ## 6 COG5150 DR1 1810 23 TF
## ----eval=FALSE---------------------------------------------------------------
# tail(roots_df)
## ----eval=FALSE---------------------------------------------------------------
# ## COGID SYMBOL ENTREZ Root TRN_element
# ## 6610 COG5640 F11 2160 19 Target
# ## 6611 KOG1418 KCNK18 338567 24 Target
# ## 6612 NOG39443 TMEM220 388335 14 Target
# ## 6613 NOG43522 C1orf170 84808 7 Target
# ## 6614 NOG127335 C16orf96 342346 6 Target
# ## 6615 NOG27843 PANX3 116337 13 Target
## ----eval=FALSE---------------------------------------------------------------
# #-- Assess root distribution by TRN_element
# wilcox.test(Root ~ TRN_element, data=roots_df)
## ----eval=FALSE---------------------------------------------------------------
# ## Wilcoxon rank sum test with continuity correction
# ## data: Root by TRN_element
# ## W = 812534, p-value = 1.6e-06
# ## alternative hypothesis: true location shift is not equal to 0
## ----eval=FALSE---------------------------------------------------------------
# #-- Set roots to display in y-axis
# roots <- c(4,8,11,13,19,21,25)
#
# #-- Set a summary function to display dispersion within the violins
# data_summary <- function(x) {
# y <- mean(x); ymin <- y-sd(x); ymax <- y+sd(x)
# return(c(y=y,ymin=ymin,ymax=ymax))
# }
#
# #-- (Figure S1) Generate violin plots showing root distribution by TRN_element
# p <- ggplot(roots_df, aes(x=TRN_element, y=Root)) +
# geom_violin(aes(fill=TRN_element), adjust=2, show.legend=F) +
# scale_y_continuous(breaks=roots, labels=paste("root",roots)) +
# scale_fill_manual(values=c("#c7eae5","#dfc27d")) +
# labs(x="TRN elements", y="Root distribution") +
# scale_x_discrete(limits=c("TF","Target"), labels=c("TFs","Targets")) +
# theme_classic() +
# theme(text=element_text(size=20)) +
# stat_summary(fun.data = data_summary)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("TF","Target")),
# label = "p.signif")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_1.pdf", width = 5.5, height = 5)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("TF","Target")),
# label = "p.signif")
# dev.off()
## ----eval=FALSE---------------------------------------------------------------
# #-- Get roots for TFs
# idx <- roots_df$TRN_element=="TF"
# tfroots <- roots_df$Root[idx]
# names(tfroots) <- roots_df$SYMBOL[idx]
#
# #-- Get roots for target genes
# regulonlist <- tni.get(rtni1st, what = "regulons", idkey = "ENTREZ")[names(tfroots)]
# targetroots <- lapply(regulonlist, function(reg){
# roots_df$Root[roots_df$ENTREZ%in%reg]
# })
#
# #-- Compute root distances between a TF and its targets
# rootdist <- sapply(names(targetroots), function(reg){
# targetroots[[reg]]-tfroots[reg]
# })
#
# #-- Compute median root distances and sort related objects
# rootdist_med <- sort(unlist(lapply(rootdist, median)), decreasing = T)
# rootdist <- rootdist[names(rootdist_med)]
# tfroots <- tfroots[names(rootdist_med)]
# targetroots <- targetroots[names(rootdist_med)]
# regulonlist <- regulonlist[names(rootdist_med)]
#
# #-- Set regulon groups based on the median root distances
# regulon_grouplist <- -sign(rootdist_med)+2
# regulon_groupnames <- c("group_a","group_b","group_c")
# regulon_groupcolors = c("#98d1f2","grey","#1c92d5")
# names(regulon_groupcolors) <- regulon_groupnames
## ----eval=FALSE---------------------------------------------------------------
# #-- (Figure S2) Generate a pie chart showing regulons grouped based on
# #-- the median distance between a TF's root and its targets' roots
# n <- as.numeric(table(regulon_grouplist))
# pie(n, labels = paste(n,"regulons"), col = regulon_groupcolors,
# border="white", cex=1.5, clockwise = TRUE, init.angle=0)
# labs <- c("TF-target genes rooted before the TF (group-a)",
# "TF-target genes rooted with the TF (group-b)",
# "TF-target genes rooted after the TF (group-c)")
# legend("bottomleft", fill = regulon_groupcolors, bty = "n", legend = labs)
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_2.pdf")
# pie(n, labels = paste(n,"regulons"), col = regulon_groupcolors,
# border="white", cex=1.5, clockwise = TRUE, init.angle=0)
# legend("bottomleft", fill = regulon_groupcolors, bty = "n", legend = labs)
# dev.off()
## ----eval=FALSE---------------------------------------------------------------
# #-- (Figure S3) Generate a boxplot showing individual regulons
# #-- sorted by the median distance to TF root
# plot.new()
# par(usr=c(c(0,length(rootdist)),range(rootdist)))
# boxplot(rootdist, horizontal= F, outline=FALSE, las=2, axes=FALSE, add=T,
# pars = list(boxwex = 0.6, boxcol=regulon_groupcolors[regulon_grouplist],
# whiskcol=regulon_groupcolors[regulon_grouplist]),
# pch="|", lty=1, lwd=0.75,
# col = regulon_groupcolors[regulon_grouplist])
# abline(h=0, lmitre=5, col="#E69F00", lwd=3, lt=2)
# par(mgp=c(2,0.1,0))
# axis(side=1, cex.axis=1.2, padj=0.5, hadj=0.5, las=1, lwd=1.5, tcl= -0.2)
# par(mgp=c(2.5,1.2,0.5))
# axis(side=2, cex.axis=1.2, padj=0.5, hadj=0.5, las=1, lwd=1.5, tcl= -0.2)
# legend("topright",legend = labs, fill = regulon_groupcolors, bty = "n")
# title(xlab = "Regulons sorted by the median distance to TF root", ylab = "Distance to TF root")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_3.pdf", width = 15, height = 4)
# plot.new()
# par(usr=c(c(0,length(rootdist)),range(rootdist)))
# boxplot(rootdist, horizontal= F, outline=FALSE, las=2, axes=FALSE, add=T,
# pars = list(boxwex = 0.6, boxcol=regulon_groupcolors[regulon_grouplist],
# whiskcol=regulon_groupcolors[regulon_grouplist]),
# pch="|", lty=1, lwd=0.75,
# col = regulon_groupcolors[regulon_grouplist])
# abline(h=0, lmitre=5, col="#E69F00", lwd=3, lt=2)
# par(mgp=c(2,0.1,0))
# axis(side=1, cex.axis=1.2, padj=0.5, hadj=0.5, las=1, lwd=1.5, tcl= -0.2)
# par(mgp=c(2.5,1.2,0.5))
# axis(side=2, cex.axis=1.2, padj=0.5, hadj=0.5, las=1, lwd=1.5, tcl= -0.2)
# legend("topright",legend = labs, fill = regulon_groupcolors, bty = "n")
# title(xlab = "Regulons sorted by the median distance to TF root", ylab = "Distance to TF root")
# dev.off()
## ----eval=FALSE---------------------------------------------------------------
# #-- Please, download the 'TcoF-DB.xlsx' file from
# #-- https://tools.sschmeier.com/tcof/browse/?type=tcof&species=human&class=all
# #-- and then load it with the 'read_excel' function
# library(readxl)
# TcoF_DB <- read_excel("TcoF-DB.xlsx")
#
# #-- Select high-confidence TcoFs according to TcoF Database
# TcoF_DB <- TcoF_DB[TcoF_DB$Type=="TcoF: class HC",]
#
# #-- Map 'TcoF_DB' to 'roots_df'
# roots_df_TcoF_DB <- roots_df
# roots_df_TcoF_DB$TRN_element <- NA
# roots_df_TcoF_DB$TRN_element[roots_df$SYMBOL %in% TcoF_DB$Symbol] <- "TcoF"
# roots_df_TcoF_DB$TRN_element[roots_df$TRN_element%in%"TF"] <- "TF"
# roots_df_TcoF_DB <- roots_df_TcoF_DB[!is.na(roots_df_TcoF_DB$TRN_element),]
# table(roots_df_TcoF_DB$TRN_element)
# ## TcoF TF
# ## 146 307
## ----eval=FALSE---------------------------------------------------------------
# #-- Assess root distribution by TRN_element
# wilcox.test(Root ~ TRN_element, data=roots_df_TcoF_DB)
## ----eval=FALSE---------------------------------------------------------------
# ## Wilcoxon rank sum test with continuity correction
# ## data: Root by TRN_element
# ## W = 22226, p-value = 0.884
# ## alternative hypothesis: true location shift is not equal to 0
## ----eval=FALSE---------------------------------------------------------------
# #-- (Figure S4) Generate violin plots showing root distribution by TRN_element
# p <- ggplot(roots_df_TcoF_DB, aes(x=TRN_element, y=Root)) +
# geom_violin(aes(fill=TRN_element), adjust=2, show.legend=F) +
# scale_y_continuous(breaks=roots, labels=paste("root",roots)) +
# scale_fill_manual(values=c("#c7eae5","#dfc27d")) +
# labs(x="TRN elements", y="Root distribution") +
# scale_x_discrete(limits=c("TF","TcoF"), labels=c("TFs","TcoFs")) +
# theme_classic() +
# theme(text=element_text(size=20)) +
# stat_summary(fun.data = data_summary)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("TF","TcoF")),
# label = "p.signif")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_4.pdf", width = 5.5, height = 5)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("TF","TcoF")),
# label = "p.signif")
# dev.off()
## ----eval=FALSE, include=FALSE------------------------------------------------
# # #-- Set repository link and file name
# # repo_link <- "https://tools.sschmeier.com/tcof/ppi/?species=human&dnl=1&f=human_tf_interactions.csv"
# # fname <- "human_tf_interactions.csv"
# #
# # #-- Download CoF-TF interactions
# # download.file(repo_link, fname)
# # CoF_TF <- read.table(fname, head = TRUE, sep=",", stringsAsFactors = FALSE)[ ,1:6]
# # colnames(CoF_TF) <- c("TF_Symbol", "TF_GeneID","TF_Type", "CoF_Symbol", "CoF_GeneID", "CoF_Type")
# # CoF_TF <- CoF_TF[!CoF_TF$CoF_Type=="TF",]
# # length(unique(CoF_TF$CoF_Symbol))
## ----eval=FALSE, include=FALSE------------------------------------------------
# # #-- Please, download the 'TcoF-DB.xlsx' file from
# # #-- https://tools.sschmeier.com/tcof/browse/?type=tf&species=human
# # #-- and then load it with the 'read_excel' function
# # library(readxl)
# # TcoF_DB <- read_excel("TcoF-DB.xlsx", col_types = "text")
# #
# # #-- Select high-confidence TcoFs according to TcoF Database
# # TcoF_DB <- TcoF_DB[TcoF_DB$Type=="TcoF: class HC",]
# # TcoF_DB <- TcoF_DB[,c("GeneID","Symbol")]
# # TcoF_DB <- data.frame(TcoF_DB, stringsAsFactors = FALSE)
# #
# # #-- Map COG IDs to TcoF_DB
# # idx <- match(TcoF_DB$GeneID,cogdata$gene_id)
# # TcoF_DB$COGID <- cogdata$cog_id[idx]
# #
# # #-- Map roots to TcoF_DB
# # results <- groot.get(ogr, what = "results")
# # idx <- match(TcoF_DB$COGID, rownames(results))
# # TcoF_DB$Root <- results$Root[idx]
# # TcoF_DB <- TcoF_DB[complete.cases(TcoF_DB),]
# # TcoF_DB$TRN_element <- "TcoF"
# #
# # #-- Load a TF source
# # data("tfsData")
# # TF_DB <- tfsData$Carro2010
# # colnames(TF_DB) <- c("GeneID","Symbol")
# #
# # #-- Map COG IDs to TF_DB
# # idx <- match(TF_DB$GeneID,cogdata$gene_id)
# # TF_DB$COGID <- cogdata$cog_id[idx]
# #
# # #-- Map roots to TF_DB
# # results <- groot.get(ogr, what = "results")
# # idx <- match(TF_DB$COGID, rownames(results))
# # TF_DB$Root <- results$Root[idx]
# # TF_DB <- TF_DB[complete.cases(TF_DB),]
# # TF_DB$TRN_element <- "TF"
# #
# # #-- Combine TF_DB and TcoF_DB
# # roots_df_TF_TcoF <- rbind(TF_DB,TcoF_DB)
# #
# # #-- Remove genes rooted at the base of the phylogenetic tree (see section 4.1)
# # roots_df_TF_TcoF <- roots_df_TF_TcoF[roots_df_TF_TcoF$Root<max(roots_df_TF_TcoF$Root),]
# # rownames(roots_df_TF_TcoF) <- 1:nrow(roots_df_TF_TcoF)
# #
# # #-- Assess root distribution by TRN_element
# # wilcox.test(Root ~ TRN_element, data=roots_df_TF_TcoF)
# # ## Wilcoxon rank sum test with continuity correction
# # ## data: Root by TRN_element
# # ## W = 43698, p-value = 0.6048
# # ## alternative hypothesis: true location shift is not equal to 0
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# #-- Compute OG's abundance, diversity and plasticity
# ogp <- gplast.preprocess(cogdata=cogdata, sspids=phyloTree$tip.label)
# ogp <- gplast(ogp)
# gpres <- gplast.get(ogp, what="results")
# head(gpres)
## ----eval=FALSE---------------------------------------------------------------
# ## abundance diversity plasticity
# ## COG0001 1.3871 0.6889 0.4150
# ## COG0002 1.1346 0.8110 0.2386
# ## COG0003 1.3243 0.9506 0.1739
# ## COG0004 4.1753 0.8880 0.5654
# ## COG0005 2.5455 0.9283 0.4182
# ## COG0006 4.3167 0.9769 0.5298
## ----eval=FALSE---------------------------------------------------------------
# #-- Map OG's abundance, diversity and plasticity to the 'roots_df' data frame
# idx <- match(roots_df$COGID,rownames(gpres))
# roots_df$Abundance <- gpres$abundance[idx]
# roots_df$Diversity <- gpres$diversity[idx]
# roots_df$Plasticity <- gpres$plasticity[idx]
#
# #-- Then map OG's abundance, diversity and plasticity to regulons
# stats_df <- lapply(regulonlist, function(reg){
# temp <- roots_df[roots_df$ENTREZ%in%reg,]
# apply(temp[ , c("Abundance","Diversity","Plasticity")], 2, mean)
# })
# stats_df <- ldply(stats_df, .id="Regulon", stringsAsFactors=FALSE)
# stats_df$regulon_groups <- regulon_grouplist[stats_df$Regulon]
# stats_df$regulon_groups <- regulon_groupnames[stats_df$regulon_groups]
## ----eval=FALSE, include=FALSE------------------------------------------------
# #-- Assess OG's abundance by regulon groups
# wilcox.test(Abundance ~ regulon_groups, data=stats_df,
# subset = regulon_groups %in% c("group_a","group_c"))
# ## Wilcoxon rank sum test with continuity correction
# ## data: Abundance by regulon_groups
# ## W = 7170, p-value = 0.1432
# ## alternative hypothesis: true location shift is not equal to 0
#
# #-- Assess OG's diversity by regulon groups
# wilcox.test(Diversity ~ regulon_groups, data=stats_df,
# subset = regulon_groups %in% c("group_a","group_c"))
# ## Wilcoxon rank sum test with continuity correction
# ## data: Diversity by regulon_groups
# ## W = 4419, p-value = 5.181e-05
# ## alternative hypothesis: true location shift is not equal to 0
#
# #-- Assess OG's plasticity by regulon groups
# wilcox.test(Plasticity ~ regulon_groups, data=stats_df,
# subset = regulon_groups %in% c("group_a","group_c"))
# ## Wilcoxon rank sum test with continuity correction
# ## data: Plasticity by regulon_groups
# ## W = 7338, p-value = 0.07175
# ## alternative hypothesis: true location shift is not equal to 0
## ----eval=FALSE, include=TRUE-------------------------------------------------
# #-- (Figure S5a) Assess OG's abundance by regulon groups
# p <- ggplot(stats_df, aes(x=regulon_groups, y=Abundance, fill=regulon_groups)) +
# geom_boxplot(show.legend=F) +
# scale_y_continuous(limits = c(0,60)) +
# scale_x_discrete(limits=c("group_a","group_c")) +
# scale_fill_manual(values=regulon_groupcolors[c("group_a","group_c")]) +
# labs(x="Regulon groups", y="OG's abundance") +
# theme(panel.grid = element_blank()) +
# theme(text=element_text(size=20), axis.line.x=element_blank())
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("group_a","group_c")),
# label = "p.signif")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_5_abundance.pdf", width = 3.6, height = 5)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("group_a","group_c")),
# label = "p.signif")
# dev.off()
## ----eval=FALSE, include=TRUE-------------------------------------------------
# #-- (Figure S5b) Assess OG's diversity by regulon groups
# p <- ggplot(stats_df, aes(x=regulon_groups, y=Diversity, fill=regulon_groups)) +
# geom_boxplot(show.legend=F) +
# scale_y_continuous(limits = c(0.5,1)) +
# scale_x_discrete(limits=c("group_a","group_c")) +
# scale_fill_manual(values=regulon_groupcolors[c("group_a","group_c")]) +
# labs(x="Regulon groups", y="OG's diversity") +
# theme(panel.grid = element_blank()) +
# theme(text=element_text(size=20), axis.line.x=element_blank())
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("group_a","group_c")),
# label = "p.signif")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_5_diversity.pdf", width = 3.6, height = 5)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("group_a","group_c")),
# label = "p.signif")
# dev.off()
## ----eval=FALSE, include=TRUE-------------------------------------------------
# #-- (Figure S5c) Assess OG's plasticity by regulon groups
# p <- ggplot(stats_df, aes(x=regulon_groups, y=Plasticity, fill=regulon_groups)) +
# geom_boxplot(show.legend=F) +
# scale_y_continuous(limits = c(0,1)) +
# scale_x_discrete(limits=c("group_a","group_c")) +
# scale_fill_manual(values=regulon_groupcolors[c("group_a","group_c")]) +
# labs(x="Regulon groups", y="OG's plasticity") +
# theme(panel.grid = element_blank()) +
# theme(text=element_text(size=20), axis.line.x=element_blank())
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("group_a","group_c")),
# label = "p.signif")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_5_plasticity.pdf", width = 3.6, height = 5)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("group_a","group_c")),
# label = "p.signif")
# dev.off()
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# data("rtniNormals")
# graph_normals <- tni.graph(rtniNormals, gtype = "rmap")
# graph_normals <- ogr2igraph(ogr, cogdata, graph_normals, idkey = "ENTREZ")
# roots_df_normals <- data.frame(COGID = V(graph_normals)$COGID,
# SYMBOL = V(graph_normals)$SYMBOL,
# ENTREZ = V(graph_normals)$ENTREZ,
# Root = V(graph_normals)$Root,
# TRN_element = c("Target","TF")[V(graph_normals)$tfs+1])
# roots_df_normals <- roots_df_normals[complete.cases(roots_df_normals),]
# roots_df_normals <- roots_df_normals[roots_df_normals$Root<max(roots_df_normals$Root),]
# rownames(roots_df_normals) <- 1:nrow(roots_df_normals)
# table(roots_df_normals$TRN_element)
## ----eval=FALSE---------------------------------------------------------------
# ## Target TF
# ## 2818 130
## ----eval=FALSE---------------------------------------------------------------
# #-- Assess root distribution by TRN_element
# wilcox.test(Root ~ TRN_element, data=roots_df_normals)
## ----eval=FALSE---------------------------------------------------------------
# ## Wilcoxon rank sum test with continuity correction
# ## data: Root by TRN_element
# ## W = 152522, p-value = 0.001148
# ## alternative hypothesis: true location shift is not equal to 0
## ----eval=FALSE---------------------------------------------------------------
# #-- Set roots to display in y-axis
# roots <- c(4,8,11,13,19,21,25)
#
# #-- Set a summary function to display dispersion within the violins
# data_summary <- function(x) {
# y <- mean(x); ymin <- y-sd(x); ymax <- y+sd(x)
# return(c(y=y,ymin=ymin,ymax=ymax))
# }
#
# #-- (Figure S6) Generate violin plots showing root distribution by TRN_element
# p <- ggplot(roots_df_normals, aes(x=TRN_element, y=Root)) +
# geom_violin(aes(fill=TRN_element), adjust=2, show.legend=F) +
# scale_y_continuous(breaks=roots, labels=paste("root",roots)) +
# scale_fill_manual(values=c("#c7eae5","#dfc27d")) +
# labs(x="TRN elements", y="Root distribution") +
# scale_x_discrete(limits=c("TF","Target"), labels=c("TFs","Targets")) +
# theme_classic() +
# theme(text=element_text(size=20)) +
# stat_summary(fun.data = data_summary)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("TF","Target")),
# label = "p.signif")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_6.pdf", width = 5.5, height = 5)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("TF","Target")),
# label = "p.signif")
# dev.off()
## ----label='Session information', eval=TRUE, echo=FALSE-----------------------
sessionInfo()
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## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
## ----eval=TRUE, message=FALSE, results='hide'---------------------------------
#-- Call packages
library(geneplast)
library(geneplast.data.string.v91)
library(RTN)
library(Fletcher2013b)
library(ggplot2)
library(ggpubr)
library(plyr)
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# #-- Load orthology data from the 'geneplast.data.string.v91' package
# data(gpdata_string_v91)
#
# #-- Create an object of class 'OGR' for a reference 'spid'
# ogr <- groot.preprocess(cogdata=cogdata, phyloTree=phyloTree, spid="9606")
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# #-- Run the 'groot' function and infer the evolutionary roots
# ogr <- groot(ogr, nPermutations=1000, verbose=TRUE)
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# #-- Load regulons
# data("rtni1st")
# tni.regulon.summary(rtni1st)
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# ## This regulatory network comprised of 809 regulons.
# ## -- DPI-filtered network:
# ## regulatoryElements Targets Edges
# ## 809 14131 47012
# ## Min. 1st Qu. Median Mean 3rd Qu. Max.
# ## 0.0 10.0 37.0 58.1 80.0 523.0
# ## -- Reference network:
# ## regulatoryElements Targets Edges
# ## 809 14131 617672
# ## Min. 1st Qu. Median Mean 3rd Qu. Max.
# ## 0 43 449 764 1245 4148
# ## ---
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# #-- Put regulons into an 'igraph' object
# #-- Note: small regulons (n<15 targets) are romeved in this step.
# graph <- tni.graph(rtni1st, gtype = "rmap")
#
# #-- Map the 'ogr' object to the 'igraph' object
# graph <- ogr2igraph(ogr, cogdata, graph, idkey = "ENTREZ")
#
# #-- Make a data frame with the gene roots
# roots_df <- data.frame(COGID = V(graph)$COGID,
# SYMBOL = V(graph)$SYMBOL,
# ENTREZ = V(graph)$ENTREZ,
# Root = V(graph)$Root,
# TRN_element = c("Target","TF")[V(graph)$tfs+1],
# stringsAsFactors = FALSE)
## ----eval=FALSE---------------------------------------------------------------
# #-- Remove NAs from missing annotation
# roots_df <- roots_df[complete.cases(roots_df),]
#
# #-- Remove genes rooted at the base of the phylogenetic tree
# roots_df <- roots_df[roots_df$Root<max(roots_df$Root),]
# rownames(roots_df) <- 1:nrow(roots_df)
#
# #-- Check TF and target counts
# table(roots_df$TRN_element)
## ----eval=FALSE---------------------------------------------------------------
# ## Target TF
# ## 6308 307
## ----eval=FALSE---------------------------------------------------------------
# head(roots_df)
## ----eval=FALSE---------------------------------------------------------------
# ## COGID SYMBOL ENTREZ Root TRN_element
# ## 1 KOG3119 CEBPG 1054 19 TF
# ## 2 KOG4217 NR4A2 4929 17 TF
# ## 3 KOG0493 EN1 2019 17 TF
# ## 4 NOG80479 TP53 7157 20 TF
# ## 5 KOG3740 GATAD2A 54815 19 TF
# ## 6 COG5150 DR1 1810 23 TF
## ----eval=FALSE---------------------------------------------------------------
# tail(roots_df)
## ----eval=FALSE---------------------------------------------------------------
# ## COGID SYMBOL ENTREZ Root TRN_element
# ## 6610 COG5640 F11 2160 19 Target
# ## 6611 KOG1418 KCNK18 338567 24 Target
# ## 6612 NOG39443 TMEM220 388335 14 Target
# ## 6613 NOG43522 C1orf170 84808 7 Target
# ## 6614 NOG127335 C16orf96 342346 6 Target
# ## 6615 NOG27843 PANX3 116337 13 Target
## ----eval=FALSE---------------------------------------------------------------
# #-- Assess root distribution by TRN_element
# wilcox.test(Root ~ TRN_element, data=roots_df)
## ----eval=FALSE---------------------------------------------------------------
# ## Wilcoxon rank sum test with continuity correction
# ## data: Root by TRN_element
# ## W = 812534, p-value = 1.6e-06
# ## alternative hypothesis: true location shift is not equal to 0
## ----eval=FALSE---------------------------------------------------------------
# #-- Set roots to display in y-axis
# roots <- c(4,8,11,13,19,21,25)
#
# #-- Set a summary function to display dispersion within the violins
# data_summary <- function(x) {
# y <- mean(x); ymin <- y-sd(x); ymax <- y+sd(x)
# return(c(y=y,ymin=ymin,ymax=ymax))
# }
#
# #-- (Figure S1) Generate violin plots showing root distribution by TRN_element
# p <- ggplot(roots_df, aes(x=TRN_element, y=Root)) +
# geom_violin(aes(fill=TRN_element), adjust=2, show.legend=F) +
# scale_y_continuous(breaks=roots, labels=paste("root",roots)) +
# scale_fill_manual(values=c("#c7eae5","#dfc27d")) +
# labs(x="TRN elements", y="Root distribution") +
# scale_x_discrete(limits=c("TF","Target"), labels=c("TFs","Targets")) +
# theme_classic() +
# theme(text=element_text(size=20)) +
# stat_summary(fun.data = data_summary)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("TF","Target")),
# label = "p.signif")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_1.pdf", width = 5.5, height = 5)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("TF","Target")),
# label = "p.signif")
# dev.off()
## ----eval=FALSE---------------------------------------------------------------
# #-- Get roots for TFs
# idx <- roots_df$TRN_element=="TF"
# tfroots <- roots_df$Root[idx]
# names(tfroots) <- roots_df$SYMBOL[idx]
#
# #-- Get roots for target genes
# regulonlist <- tni.get(rtni1st, what = "regulons", idkey = "ENTREZ")[names(tfroots)]
# targetroots <- lapply(regulonlist, function(reg){
# roots_df$Root[roots_df$ENTREZ%in%reg]
# })
#
# #-- Compute root distances between a TF and its targets
# rootdist <- sapply(names(targetroots), function(reg){
# targetroots[[reg]]-tfroots[reg]
# })
#
# #-- Compute median root distances and sort related objects
# rootdist_med <- sort(unlist(lapply(rootdist, median)), decreasing = T)
# rootdist <- rootdist[names(rootdist_med)]
# tfroots <- tfroots[names(rootdist_med)]
# targetroots <- targetroots[names(rootdist_med)]
# regulonlist <- regulonlist[names(rootdist_med)]
#
# #-- Set regulon groups based on the median root distances
# regulon_grouplist <- -sign(rootdist_med)+2
# regulon_groupnames <- c("group_a","group_b","group_c")
# regulon_groupcolors = c("#98d1f2","grey","#1c92d5")
# names(regulon_groupcolors) <- regulon_groupnames
## ----eval=FALSE---------------------------------------------------------------
# #-- (Figure S2) Generate a pie chart showing regulons grouped based on
# #-- the median distance between a TF's root and its targets' roots
# n <- as.numeric(table(regulon_grouplist))
# pie(n, labels = paste(n,"regulons"), col = regulon_groupcolors,
# border="white", cex=1.5, clockwise = TRUE, init.angle=0)
# labs <- c("TF-target genes rooted before the TF (group-a)",
# "TF-target genes rooted with the TF (group-b)",
# "TF-target genes rooted after the TF (group-c)")
# legend("bottomleft", fill = regulon_groupcolors, bty = "n", legend = labs)
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_2.pdf")
# pie(n, labels = paste(n,"regulons"), col = regulon_groupcolors,
# border="white", cex=1.5, clockwise = TRUE, init.angle=0)
# legend("bottomleft", fill = regulon_groupcolors, bty = "n", legend = labs)
# dev.off()
## ----eval=FALSE---------------------------------------------------------------
# #-- (Figure S3) Generate a boxplot showing individual regulons
# #-- sorted by the median distance to TF root
# plot.new()
# par(usr=c(c(0,length(rootdist)),range(rootdist)))
# boxplot(rootdist, horizontal= F, outline=FALSE, las=2, axes=FALSE, add=T,
# pars = list(boxwex = 0.6, boxcol=regulon_groupcolors[regulon_grouplist],
# whiskcol=regulon_groupcolors[regulon_grouplist]),
# pch="|", lty=1, lwd=0.75,
# col = regulon_groupcolors[regulon_grouplist])
# abline(h=0, lmitre=5, col="#E69F00", lwd=3, lt=2)
# par(mgp=c(2,0.1,0))
# axis(side=1, cex.axis=1.2, padj=0.5, hadj=0.5, las=1, lwd=1.5, tcl= -0.2)
# par(mgp=c(2.5,1.2,0.5))
# axis(side=2, cex.axis=1.2, padj=0.5, hadj=0.5, las=1, lwd=1.5, tcl= -0.2)
# legend("topright",legend = labs, fill = regulon_groupcolors, bty = "n")
# title(xlab = "Regulons sorted by the median distance to TF root", ylab = "Distance to TF root")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_3.pdf", width = 15, height = 4)
# plot.new()
# par(usr=c(c(0,length(rootdist)),range(rootdist)))
# boxplot(rootdist, horizontal= F, outline=FALSE, las=2, axes=FALSE, add=T,
# pars = list(boxwex = 0.6, boxcol=regulon_groupcolors[regulon_grouplist],
# whiskcol=regulon_groupcolors[regulon_grouplist]),
# pch="|", lty=1, lwd=0.75,
# col = regulon_groupcolors[regulon_grouplist])
# abline(h=0, lmitre=5, col="#E69F00", lwd=3, lt=2)
# par(mgp=c(2,0.1,0))
# axis(side=1, cex.axis=1.2, padj=0.5, hadj=0.5, las=1, lwd=1.5, tcl= -0.2)
# par(mgp=c(2.5,1.2,0.5))
# axis(side=2, cex.axis=1.2, padj=0.5, hadj=0.5, las=1, lwd=1.5, tcl= -0.2)
# legend("topright",legend = labs, fill = regulon_groupcolors, bty = "n")
# title(xlab = "Regulons sorted by the median distance to TF root", ylab = "Distance to TF root")
# dev.off()
## ----eval=FALSE---------------------------------------------------------------
# #-- Please, download the 'TcoF-DB.xlsx' file from
# #-- https://tools.sschmeier.com/tcof/browse/?type=tcof&species=human&class=all
# #-- and then load it with the 'read_excel' function
# library(readxl)
# TcoF_DB <- read_excel("TcoF-DB.xlsx")
#
# #-- Select high-confidence TcoFs according to TcoF Database
# TcoF_DB <- TcoF_DB[TcoF_DB$Type=="TcoF: class HC",]
#
# #-- Map 'TcoF_DB' to 'roots_df'
# roots_df_TcoF_DB <- roots_df
# roots_df_TcoF_DB$TRN_element <- NA
# roots_df_TcoF_DB$TRN_element[roots_df$SYMBOL %in% TcoF_DB$Symbol] <- "TcoF"
# roots_df_TcoF_DB$TRN_element[roots_df$TRN_element%in%"TF"] <- "TF"
# roots_df_TcoF_DB <- roots_df_TcoF_DB[!is.na(roots_df_TcoF_DB$TRN_element),]
# table(roots_df_TcoF_DB$TRN_element)
# ## TcoF TF
# ## 146 307
## ----eval=FALSE---------------------------------------------------------------
# #-- Assess root distribution by TRN_element
# wilcox.test(Root ~ TRN_element, data=roots_df_TcoF_DB)
## ----eval=FALSE---------------------------------------------------------------
# ## Wilcoxon rank sum test with continuity correction
# ## data: Root by TRN_element
# ## W = 22226, p-value = 0.884
# ## alternative hypothesis: true location shift is not equal to 0
## ----eval=FALSE---------------------------------------------------------------
# #-- (Figure S4) Generate violin plots showing root distribution by TRN_element
# p <- ggplot(roots_df_TcoF_DB, aes(x=TRN_element, y=Root)) +
# geom_violin(aes(fill=TRN_element), adjust=2, show.legend=F) +
# scale_y_continuous(breaks=roots, labels=paste("root",roots)) +
# scale_fill_manual(values=c("#c7eae5","#dfc27d")) +
# labs(x="TRN elements", y="Root distribution") +
# scale_x_discrete(limits=c("TF","TcoF"), labels=c("TFs","TcoFs")) +
# theme_classic() +
# theme(text=element_text(size=20)) +
# stat_summary(fun.data = data_summary)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("TF","TcoF")),
# label = "p.signif")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_4.pdf", width = 5.5, height = 5)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("TF","TcoF")),
# label = "p.signif")
# dev.off()
## ----eval=FALSE, include=FALSE------------------------------------------------
# # #-- Set repository link and file name
# # repo_link <- "https://tools.sschmeier.com/tcof/ppi/?species=human&dnl=1&f=human_tf_interactions.csv"
# # fname <- "human_tf_interactions.csv"
# #
# # #-- Download CoF-TF interactions
# # download.file(repo_link, fname)
# # CoF_TF <- read.table(fname, head = TRUE, sep=",", stringsAsFactors = FALSE)[ ,1:6]
# # colnames(CoF_TF) <- c("TF_Symbol", "TF_GeneID","TF_Type", "CoF_Symbol", "CoF_GeneID", "CoF_Type")
# # CoF_TF <- CoF_TF[!CoF_TF$CoF_Type=="TF",]
# # length(unique(CoF_TF$CoF_Symbol))
## ----eval=FALSE, include=FALSE------------------------------------------------
# # #-- Please, download the 'TcoF-DB.xlsx' file from
# # #-- https://tools.sschmeier.com/tcof/browse/?type=tf&species=human
# # #-- and then load it with the 'read_excel' function
# # library(readxl)
# # TcoF_DB <- read_excel("TcoF-DB.xlsx", col_types = "text")
# #
# # #-- Select high-confidence TcoFs according to TcoF Database
# # TcoF_DB <- TcoF_DB[TcoF_DB$Type=="TcoF: class HC",]
# # TcoF_DB <- TcoF_DB[,c("GeneID","Symbol")]
# # TcoF_DB <- data.frame(TcoF_DB, stringsAsFactors = FALSE)
# #
# # #-- Map COG IDs to TcoF_DB
# # idx <- match(TcoF_DB$GeneID,cogdata$gene_id)
# # TcoF_DB$COGID <- cogdata$cog_id[idx]
# #
# # #-- Map roots to TcoF_DB
# # results <- groot.get(ogr, what = "results")
# # idx <- match(TcoF_DB$COGID, rownames(results))
# # TcoF_DB$Root <- results$Root[idx]
# # TcoF_DB <- TcoF_DB[complete.cases(TcoF_DB),]
# # TcoF_DB$TRN_element <- "TcoF"
# #
# # #-- Load a TF source
# # data("tfsData")
# # TF_DB <- tfsData$Carro2010
# # colnames(TF_DB) <- c("GeneID","Symbol")
# #
# # #-- Map COG IDs to TF_DB
# # idx <- match(TF_DB$GeneID,cogdata$gene_id)
# # TF_DB$COGID <- cogdata$cog_id[idx]
# #
# # #-- Map roots to TF_DB
# # results <- groot.get(ogr, what = "results")
# # idx <- match(TF_DB$COGID, rownames(results))
# # TF_DB$Root <- results$Root[idx]
# # TF_DB <- TF_DB[complete.cases(TF_DB),]
# # TF_DB$TRN_element <- "TF"
# #
# # #-- Combine TF_DB and TcoF_DB
# # roots_df_TF_TcoF <- rbind(TF_DB,TcoF_DB)
# #
# # #-- Remove genes rooted at the base of the phylogenetic tree (see section 4.1)
# # roots_df_TF_TcoF <- roots_df_TF_TcoF[roots_df_TF_TcoF$Root<max(roots_df_TF_TcoF$Root),]
# # rownames(roots_df_TF_TcoF) <- 1:nrow(roots_df_TF_TcoF)
# #
# # #-- Assess root distribution by TRN_element
# # wilcox.test(Root ~ TRN_element, data=roots_df_TF_TcoF)
# # ## Wilcoxon rank sum test with continuity correction
# # ## data: Root by TRN_element
# # ## W = 43698, p-value = 0.6048
# # ## alternative hypothesis: true location shift is not equal to 0
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# #-- Compute OG's abundance, diversity and plasticity
# ogp <- gplast.preprocess(cogdata=cogdata, sspids=phyloTree$tip.label)
# ogp <- gplast(ogp)
# gpres <- gplast.get(ogp, what="results")
# head(gpres)
## ----eval=FALSE---------------------------------------------------------------
# ## abundance diversity plasticity
# ## COG0001 1.3871 0.6889 0.4150
# ## COG0002 1.1346 0.8110 0.2386
# ## COG0003 1.3243 0.9506 0.1739
# ## COG0004 4.1753 0.8880 0.5654
# ## COG0005 2.5455 0.9283 0.4182
# ## COG0006 4.3167 0.9769 0.5298
## ----eval=FALSE---------------------------------------------------------------
# #-- Map OG's abundance, diversity and plasticity to the 'roots_df' data frame
# idx <- match(roots_df$COGID,rownames(gpres))
# roots_df$Abundance <- gpres$abundance[idx]
# roots_df$Diversity <- gpres$diversity[idx]
# roots_df$Plasticity <- gpres$plasticity[idx]
#
# #-- Then map OG's abundance, diversity and plasticity to regulons
# stats_df <- lapply(regulonlist, function(reg){
# temp <- roots_df[roots_df$ENTREZ%in%reg,]
# apply(temp[ , c("Abundance","Diversity","Plasticity")], 2, mean)
# })
# stats_df <- ldply(stats_df, .id="Regulon", stringsAsFactors=FALSE)
# stats_df$regulon_groups <- regulon_grouplist[stats_df$Regulon]
# stats_df$regulon_groups <- regulon_groupnames[stats_df$regulon_groups]
## ----eval=FALSE, include=FALSE------------------------------------------------
# #-- Assess OG's abundance by regulon groups
# wilcox.test(Abundance ~ regulon_groups, data=stats_df,
# subset = regulon_groups %in% c("group_a","group_c"))
# ## Wilcoxon rank sum test with continuity correction
# ## data: Abundance by regulon_groups
# ## W = 7170, p-value = 0.1432
# ## alternative hypothesis: true location shift is not equal to 0
#
# #-- Assess OG's diversity by regulon groups
# wilcox.test(Diversity ~ regulon_groups, data=stats_df,
# subset = regulon_groups %in% c("group_a","group_c"))
# ## Wilcoxon rank sum test with continuity correction
# ## data: Diversity by regulon_groups
# ## W = 4419, p-value = 5.181e-05
# ## alternative hypothesis: true location shift is not equal to 0
#
# #-- Assess OG's plasticity by regulon groups
# wilcox.test(Plasticity ~ regulon_groups, data=stats_df,
# subset = regulon_groups %in% c("group_a","group_c"))
# ## Wilcoxon rank sum test with continuity correction
# ## data: Plasticity by regulon_groups
# ## W = 7338, p-value = 0.07175
# ## alternative hypothesis: true location shift is not equal to 0
## ----eval=FALSE, include=TRUE-------------------------------------------------
# #-- (Figure S5a) Assess OG's abundance by regulon groups
# p <- ggplot(stats_df, aes(x=regulon_groups, y=Abundance, fill=regulon_groups)) +
# geom_boxplot(show.legend=F) +
# scale_y_continuous(limits = c(0,60)) +
# scale_x_discrete(limits=c("group_a","group_c")) +
# scale_fill_manual(values=regulon_groupcolors[c("group_a","group_c")]) +
# labs(x="Regulon groups", y="OG's abundance") +
# theme(panel.grid = element_blank()) +
# theme(text=element_text(size=20), axis.line.x=element_blank())
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("group_a","group_c")),
# label = "p.signif")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_5_abundance.pdf", width = 3.6, height = 5)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("group_a","group_c")),
# label = "p.signif")
# dev.off()
## ----eval=FALSE, include=TRUE-------------------------------------------------
# #-- (Figure S5b) Assess OG's diversity by regulon groups
# p <- ggplot(stats_df, aes(x=regulon_groups, y=Diversity, fill=regulon_groups)) +
# geom_boxplot(show.legend=F) +
# scale_y_continuous(limits = c(0.5,1)) +
# scale_x_discrete(limits=c("group_a","group_c")) +
# scale_fill_manual(values=regulon_groupcolors[c("group_a","group_c")]) +
# labs(x="Regulon groups", y="OG's diversity") +
# theme(panel.grid = element_blank()) +
# theme(text=element_text(size=20), axis.line.x=element_blank())
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("group_a","group_c")),
# label = "p.signif")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_5_diversity.pdf", width = 3.6, height = 5)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("group_a","group_c")),
# label = "p.signif")
# dev.off()
## ----eval=FALSE, include=TRUE-------------------------------------------------
# #-- (Figure S5c) Assess OG's plasticity by regulon groups
# p <- ggplot(stats_df, aes(x=regulon_groups, y=Plasticity, fill=regulon_groups)) +
# geom_boxplot(show.legend=F) +
# scale_y_continuous(limits = c(0,1)) +
# scale_x_discrete(limits=c("group_a","group_c")) +
# scale_fill_manual(values=regulon_groupcolors[c("group_a","group_c")]) +
# labs(x="Regulon groups", y="OG's plasticity") +
# theme(panel.grid = element_blank()) +
# theme(text=element_text(size=20), axis.line.x=element_blank())
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("group_a","group_c")),
# label = "p.signif")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_5_plasticity.pdf", width = 3.6, height = 5)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("group_a","group_c")),
# label = "p.signif")
# dev.off()
## ----eval=FALSE, message=FALSE, warning=FALSE---------------------------------
# data("rtniNormals")
# graph_normals <- tni.graph(rtniNormals, gtype = "rmap")
# graph_normals <- ogr2igraph(ogr, cogdata, graph_normals, idkey = "ENTREZ")
# roots_df_normals <- data.frame(COGID = V(graph_normals)$COGID,
# SYMBOL = V(graph_normals)$SYMBOL,
# ENTREZ = V(graph_normals)$ENTREZ,
# Root = V(graph_normals)$Root,
# TRN_element = c("Target","TF")[V(graph_normals)$tfs+1])
# roots_df_normals <- roots_df_normals[complete.cases(roots_df_normals),]
# roots_df_normals <- roots_df_normals[roots_df_normals$Root<max(roots_df_normals$Root),]
# rownames(roots_df_normals) <- 1:nrow(roots_df_normals)
# table(roots_df_normals$TRN_element)
## ----eval=FALSE---------------------------------------------------------------
# ## Target TF
# ## 2818 130
## ----eval=FALSE---------------------------------------------------------------
# #-- Assess root distribution by TRN_element
# wilcox.test(Root ~ TRN_element, data=roots_df_normals)
## ----eval=FALSE---------------------------------------------------------------
# ## Wilcoxon rank sum test with continuity correction
# ## data: Root by TRN_element
# ## W = 152522, p-value = 0.001148
# ## alternative hypothesis: true location shift is not equal to 0
## ----eval=FALSE---------------------------------------------------------------
# #-- Set roots to display in y-axis
# roots <- c(4,8,11,13,19,21,25)
#
# #-- Set a summary function to display dispersion within the violins
# data_summary <- function(x) {
# y <- mean(x); ymin <- y-sd(x); ymax <- y+sd(x)
# return(c(y=y,ymin=ymin,ymax=ymax))
# }
#
# #-- (Figure S6) Generate violin plots showing root distribution by TRN_element
# p <- ggplot(roots_df_normals, aes(x=TRN_element, y=Root)) +
# geom_violin(aes(fill=TRN_element), adjust=2, show.legend=F) +
# scale_y_continuous(breaks=roots, labels=paste("root",roots)) +
# scale_fill_manual(values=c("#c7eae5","#dfc27d")) +
# labs(x="TRN elements", y="Root distribution") +
# scale_x_discrete(limits=c("TF","Target"), labels=c("TFs","Targets")) +
# theme_classic() +
# theme(text=element_text(size=20)) +
# stat_summary(fun.data = data_summary)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("TF","Target")),
# label = "p.signif")
## ----eval=FALSE, include=FALSE------------------------------------------------
# pdf(file = "geneplast_Trefflich2019_6.pdf", width = 5.5, height = 5)
# p + stat_compare_means(method="wilcox.test",
# comparisons =list(c("TF","Target")),
# label = "p.signif")
# dev.off()
## ----label='Session information', eval=TRUE, echo=FALSE-----------------------
sessionInfo()
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