DF Updated

inst/manuscript/dermalFibroblasts-netDifferences.R

@@ -100,19 +100,20 @@ sY <- assignDirectionNetworK(igraphNetwork = sY, countMatrix = mY, bootR = 100)
 sO <- assignDirectionNetworK(igraphNetwork = sO, countMatrix = mO, bootR = 100)
 
 uNet <- igraph::union(sY,sO)
-set.seed(3)
-lNet <- igraph::layout.graphopt(uNet, charge = 1e-3)
+set.seed(1)
+lNet <- igraph::layout.graphopt(uNet, charge = 1e-2)
+plot(uNet, layout = lNet)
 rownames(lNet) <- names(V(uNet))
-lNet[names(V(sO)),] <- lNet[names(V(sO)),]*4
-mCoord <- tkplot(uNet, layout= lNet)
-
-lNet <- tk_coords(mCoord)
-write.table(lNet, 'figures/coordinatesDFplot.tsv')
+#lNet[names(V(sO)),] <- lNet[names(V(sO)),]*4
+#mCoord <- tkplot(uNet, layout= lNet)
+
+#lNet <- tk_coords(mCoord)
+#write.table(lNet, 'figures/coordinatesDFplot.tsv')
+lNet <- read.table('figures/coordinatesDFplot.tsv')
 lNet <- t(t(lNet)/apply(abs(lNet),2,max))
 rownames(lNet) <- names(V(uNet))
 plot(uNet, layout = lNet)
-lNet[,1] <- lNet[,1]*3.5
-lNet[,2] <- lNet[,2]*1.3
+lNet[,] <- lNet[,] * -1.5
 gY <- names(V(sY))
 gO <- names(V(sO))
 
@@ -146,8 +147,8 @@ myCircle <- function(coords, v=NULL, params) {
 
 add.vertex.shape("fcircle", clip=igraph.shape.noclip,plot=myCircle, parameters=list(vertex.frame.color=1, vertex.frame.width=1))
 
-png('figures/dfDiffNetworks.png', width = 6000, height = 3000, res = 300)
-par(mfrow=c(1,2))
+png('figures/dfDiffNetworks.png', width = 6000, height = 3000, res = 300, pointsize = 20, bg = NA)
+par(mfrow=c(1,2), mar=c(1,1,1,1))
 fColor <- ifelse(gY %in% gO, 'darkgoldenrod', NA)
 fColor[(gY %in% dC) & fColor == 'darkgoldenrod'] <- 'forestgreen'
 plot(sY, layout = lNet[names(V(sY)),], vertex.shape="fcircle", vertex.frame.color=fColor, vertex.frame.width=12, vertex.label = NA, edge.width = NA, edge.arrow.size = 0, rescale = FALSE, xlim = c(min(lNet[,1]), max(lNet[,1])), ylim=c(min(lNet[,2]), max(lNet[,2])), mark.groups = which(gY %in% gO), mark.col="#C5E5E7", mark.border=NA)

inst/manuscript/figures/coordinatesDFplot.tsv

@@ -1,43 +1,43 @@
 "V1" "V2"
-"S100A11" 1.82424242424242 1.11543209876543
-"ANXA5" 1.93030303030303 0.533641975308642
-"RPS18" 2.55818181818182 0.886728395061729
-"RPS12" 2.57515151515152 1.07932098765432
-"ANXA1" 2.27818181818182 0.90679012345679
-"LDHA" 1.61212121212121 0.878703703703704
-"CFL1" 2.15090909090909 0.625925925925926
-"TPI1" 2.21454545454545 1.3
-"CD63" 2.00242424242424 0.958950617283951
-"MYL6" 2.20181818181818 1.07932098765432
-"LGALS3" 1.71393939393939 0.690123456790124
-"B2M" 2.1169696969697 0.425308641975309
-"ANXA2" 1.97272727272727 0.746296296296296
-"RPLP1" 2.57515151515152 1.27993827160494
-"ALDOA" 2.01939393939394 1.27191358024691
-"RPL13" 2.47333333333333 0.71820987654321
-"UBB" 1.73515151515152 0.958950617283951
-"RPL11" 2.67484848484848 0
-"RPS8" 3.35363636363636 0.545679012345679
-"RPL15" 3.29636363636364 0.710185185185185
-"RPS3A" 3.04181818181818 0.870679012345679
-"RPS14" 2.79575757575758 0.890740740740741
-"RPL10A" 2.37630417140533 0.508833489644248
-"RPS4X" 2.75757575757576 1.07530864197531
-"RPL10" 2.88484848484848 1.22376543209877
-"RPL8" 2.61426584072527 0.20867815994969
-"RPS6" 3.11393939393939 0.58179012345679
-"RPL12" 3.27515151515152 1.2037037037037
-"RPS3" 3.24969696969697 0.413271604938272
-"RPL6" 2.28315022668098 0.266458293080652
-"RPLP0" 3.02909090909091 0.381172839506173
-"RPS2" 2.75414173735312 0.345510006272274
-"TNFRSF12A" 3.5 0.898765432098765
-"H3F3B" 2.91030303030303 0.710185185185185
-"OAZ1" 2.93787878787879 0.140432098765432
-"RPL13A" 2.98878787878788 1.04722222222222
-"RPS9" 3.22 0.975
-"RPL3" 2.69606060606061 0.730246913580247
-"MT-ND1" 2.54545454545455 0.349074074074074
-"MT-CO1" 2.63878787878788 0.525617283950617
-"MT-CO3" 3.15424242424242 0.228703703703704
-"MT-ND4" 2.85727272727273 0.509567901234568
+"S100A11" -1.11965134706815 -0.183807439824945
+"ANXA5" -1.40966719492868 -0.393873085339168
+"RPS18" -0.914025356576862 -0.705689277899344
+"RPS12" -0.752377179080824 -0.413566739606127
+"ANXA1" -0.955625990491284 -0.210065645514223
+"LDHA" -1.22424722662441 0
+"CFL1" -1.16006339144216 -0.62363238512035
+"TPI1" -1.03882725832013 -0.551422319474836
+"CD63" -1.47147385103011 -0.567833698030635
+"MYL6" -1.25277337559429 -0.777899343544858
+"LGALS3" -1.28843106180666 -0.223194748358862
+"B2M" -1.36450079239303 -0.682713347921225
+"ANXA2" -1.2337559429477 -0.390590809628009
+"RPLP1" -0.842709984152139 -0.557986870897155
+"ALDOA" -1.5 -0.154266958424508
+"RPL13" -1.01980982567353 -0.833698030634573
+"UBB" -1.07210776545166 -0.390590809628009
+"RPL11" -0.16877971473851 -1.17177242888403
+"RPS8" -0.556259904912837 -0.919037199124726
+"RPL15" -0.140253565768621 -0.515317286652079
+"RPS3A" -0.539619651347068 -0.439824945295405
+"RPS14" -0.282884310618067 -1.37855579868709
+"RPL10A" -0.993660855784469 -1.03719912472648
+"RPS4X" -0.344690966719493 -0.38074398249453
+"RPL10" -0.872424722662441 -1.37855579868709
+"RPL8" -0.765451664025357 -1.2144420131291
+"RPS6" -0.323296354992076 -1.07002188183807
+"RPL12" -0.594294770206022 -0.213347921225383
+"RPS3" -0.102218700475436 -0.932166301969366
+"RPL6" -0.972266244057052 -1.21772428884026
+"RPLP0" -0.446909667194929 -1.2308533916849
+"RPS2" -0.59904912836767 -1.14223194748359
+"TNFRSF12A" -0.375594294770206 -0.164113785557987
+"H3F3B" -0.758320126782884 -0.764770240700219
+"OAZ1" -0.692947702060222 -1.41137855579869
+"RPL13A" -0.86053882725832 -0.915754923413567
+"RPS9" -0.656101426307448 -0.590809628008753
+"RPL3" -0.698890649762282 -1.0109409190372
+"MT-ND1" -0.292393026941363 -0.617067833698031
+"MT-CO1" -0.527733755942948 -0.731947483588621
+"MT-CO3" -0.465927099841521 -1.5
+"MT-ND4" -0.337559429477021 -0.86980306345733