Merge pull request #4 from solislemuslab/dev

Added changes to the sticker

real_data/alphavsmean.R

@@ -6,16 +6,37 @@ soil <- soil[order(soil$mu),]
 soil$genus <- factor(soil$X, levels = (as.character(soil$X)))
 human <- human[order(human$mu),]
 human$genus <- factor(human$X, levels = (as.character(human$X)))
+
 gsoil <- ggplot(data = soil,aes(x=genus,y=alpha_cent)) + 
-  geom_bar( stat = "identity") + 
+  geom_bar( stat = "identity", fill="chocolate") + 
   ylab("alpha centrality") +
-  xlab("soil")+
+  xlab("")+ ggtitle("Soil") +
+  theme(
+    plot.title = element_text(hjust=0.5, size=rel(1.5)),
+    axis.title.x = element_text(size=rel(1.2)),
+    axis.title.y = element_text(size=rel(1.2), angle=90, vjust=0.5, hjust=0.5),
+    axis.text.x = element_text(colour="grey49", size=rel(1.0), angle=0, face="plain"),
+    axis.text.y = element_text(colour="grey49", size=rel(1.2), angle=0, face="plain"),
+    panel.background = element_blank(),
+    axis.line = element_line(colour = "grey"),
+    strip.text = element_text(size = 17)
+  ) +
   coord_flip()
 
 ghuman <- ggplot(data = human,aes(x=genus,y=alpha_cent)) + 
-  geom_bar( stat = "identity") + 
+  geom_bar( stat = "identity", fill="gold3") + 
   ylab("alpha centrality") +
-  xlab("gut") +
+  xlab("") + ggtitle("Human gut") +
+  theme(
+    plot.title = element_text(hjust=0.5, size=rel(1.5)),
+    axis.title.x = element_text(size=rel(1.2)),
+    axis.title.y = element_text(size=rel(1.2), angle=90, vjust=0.5, hjust=0.5),
+    axis.text.x = element_text(colour="grey49", size=rel(1.0), angle=0, face="plain"),
+    axis.text.y = element_text(colour="grey49", size=rel(1.2), angle=0, face="plain"),
+    panel.background = element_blank(),
+    axis.line = element_line(colour = "grey"),
+    strip.text = element_text(size = 17)
+  ) +
   coord_flip() 
 
 
@@ -24,8 +45,8 @@ ggpubr::ggarrange(ghuman,gsoil,
           ncol = 2, nrow = 1)
 
 
-ggsave("./real_data/alpha_cent_vs_mu.pdf", width = 9, height = 4, scale = 0.8)
-
+#ggsave("./real_data/alpha_cent_vs_mu.pdf", width = 9, height = 4, scale = 0.8)
+ggsave("alpha_cent_vs_mu2.pdf", width = 10, height = 5, scale = 0.8)  
 
 
 cor.test(human$mu, human$alpha_cent,

tests/Formal/Accurancy/Graph_ploter.R

@@ -16,28 +16,39 @@ graphss <- lapply(1:6, function(i){
 graphss <- Reduce(stack, graphss)
 names(graphss) <- paste0("model",1:6)
 
-gplot(graphss) +
-  geom_tile(aes(fill = value)) +
-  facet_wrap(~ variable) +
+#blue: "#0072B2", 
+#red: "#990000"
+
+p <- gplot(graphss) +
+  geom_tile(aes(fill = value), color="grey65") +
+  facet_grid(~ variable) +
   scale_fill_gradient2(#low = "#0339ce",
                       #high =  "#fdcf18",
-                      low = "red",
-                      #mid = "white",
-                      mid = "grey95",
-                      high = "blue",
+                      #low = "blue",
+                      low = "#0072B2",
+                      mid = "white",
+                      #mid = "grey95",
+                      #high = "red",
+                      high = "#990000",
                       midpoint = 0,
                       na.value="transparent") +
   labs(fill = "value", x = "", y="") +
-  theme(text = element_text(size=14), 
+  theme(text = element_text(size=20), 
         axis.text.x = element_blank(),
         axis.text.y = element_blank(),
         axis.ticks = element_blank(),
-        plot.margin = margin(.15, .15, .15, .15, "cm"))+
+        plot.margin = margin(.15, .15, .15, .15, "cm"),
+        #legend.position = "bottom",
+        legend.title = element_blank())+
   theme(
     panel.background = element_rect(fill = "transparent"), # bg of the panel
     plot.background = element_rect(fill = "transparent", color = NA), # bg of the plot
     legend.background = element_rect(fill = "transparent")#, # get rid of legend bg
     #legend.box.background = element_rect(fill = "transparent") # get rid of legend panel bg
   )
 
-ggsave("./simu_graphs.pdf",width = 10.5,height=7, scale = 0.8)
+#ggsave("./simu_graphs.pdf",width = 10.5,height=7, scale = 0.8)
+
+pdf("model-grid.pdf", height=3, width=18)
+p
+dev.off()

tests/sticker.R

@@ -26,3 +26,34 @@ ww
 ggsave("CARlasso.png",width = 1,height = 1, unit = "in", dpi = 500, scale = 1)
 
 sticker(pp, package = "CARlasso", s_width = 2.3, s_height=2.3, s_x=0.96, s_y=0.65, h_fill = "#4e8ff0", p_y = 1.5, p_size = 15.5) 
+
+
+## New sticker:
+# CAR-LASSO
+library(CARlasso)
+library(ggplot2)
+library(hexSticker)
+
+#example(CARlasso)
+set.seed(1234)
+dt <- simu_AR1(n=100,k=4, rho=0.7)
+car_res <- CARlasso(y1+y2+y3+y4~x1+x2+x3, data = dt, adaptive = TRUE)
+
+car_res$nodes$predictors <- rep("", 3)
+car_res$nodes$response <- rep("", 4)
+p <- plot(car_res)
+pp <- p + theme(legend.position = "none") +
+  theme(
+    panel.background = element_rect(fill = "transparent",color = NA), # bg of the panel
+    plot.background = element_rect(fill = "transparent", color = NA), # bg of the plot
+    panel.grid.major = element_blank(), # get rid of major grid
+    panel.grid.minor = element_blank(), # get rid of minor grid
+    legend.background = element_rect(fill = "transparent"), # get rid of legend bg
+    legend.box.background = element_rect(fill = "transparent"), # get rid of legend panel bg
+    legend.key = element_rect(fill = "transparent", colour = NA), # get rid of key legend fill, and of the surrounding
+    axis.line = element_line(colour = NA) # adding a black line for x and y axis
+  )
+
+
+ww <- sticker(pp, package = "CARlasso", s_width = 1.83, s_height=1.83, s_x=1.05, s_y=0.8, h_fill = "#edeff2", p_y = 1.6, p_color="black", p_size=15, h_color="#9d9d9e")
+ww