add fig S5

README.md

@@ -5,6 +5,7 @@ This repository contains scripts for recreation of the figures from the SC3 pape
 
 [cowplot](https://cran.r-project.org/web/packages/cowplot/index.html)  
 [dplyr](https://cran.r-project.org/web/packages/dplyr/index.html)
+[googleVis](https://cran.r-project.org/web/packages/googleVis/index.html)
 
 ### Fig. 1
 [data_c](data/1c.csv)  
@@ -52,6 +53,17 @@ This repository contains scripts for recreation of the figures from the SC3 pape
 
 ![](jpeg/S4.jpeg)
 
+### Fig. S5
+[data_a](data/S5a.csv)  
+[data_b](data/S5b.csv)  
+[html_b](data/S5b.html)  
+[script_a](S4a.R)  
+[script_b](S4b.R)  
+[pdf_a](pdf/S5a.pdf)  
+[pdf_b](pdf/S5b.pdf)
+
+![](jpeg/S4.jpeg)
+
 ## Session Info
 
 ```
@@ -66,10 +78,10 @@ attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
-[1] dplyr_0.5.0   cowplot_0.7.0 ggplot2_2.2.1
+[1] googleVis_0.6.1 dplyr_0.5.0     cowplot_0.7.0   ggplot2_2.2.1  
 
 loaded via a namespace (and not attached):
- [1] colorspace_1.3-1 scales_0.4.1     magrittr_1.5     R6_2.2.0         assertthat_0.1   lazyeval_0.2.0  
- [7] plyr_1.8.4       DBI_0.5-1        tools_3.4.0      gtable_0.2.0     tibble_1.2       Rcpp_0.12.8     
-[13] grid_3.4.0       munsell_0.4.3     
+ [1] Rcpp_0.12.8      codetools_0.2-15 assertthat_0.1   grid_3.4.0       plyr_1.8.4       R6_2.2.0        
+ [7] jsonlite_1.1     gtable_0.2.0     DBI_0.5-1        magrittr_1.5     scales_0.4.1     lazyeval_0.2.0  
+[13] tools_3.4.0      munsell_0.4.3    colorspace_1.3-1 tibble_1.2   
 ```

S5a.R

@@ -0,0 +1,12 @@
+library(cowplot)
+
+d <- read.csv("data/S5a.csv")
+
+p <- ggplot(d, aes(variable, value)) +
+    geom_boxplot() +
+    labs(x = "", y = "ARI") +
+    ylim(0, 1) +
+    theme_classic(base_size = 8)
+
+ggsave("pdf/S5a.pdf", w = 4, h = 6)
+ggsave("jpeg/S5a.jpeg", w = 4, h = 6)

S5b.R

@@ -0,0 +1,85 @@
+library(googleVis)
+library(dplyr)
+library(reshape2)
+
+d <- read.csv("data/S5b.csv")
+
+reference <- d$SEURAT
+clusters <- d$SC3
+
+colors <- c('#FF0000',
+            '#FFA500',
+            '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000', '#008000',
+            '#57A5D6', '#57A5D6',
+            '#0000FF', '#0000FF', '#0000FF', '#0000FF', '#0000FF', '#0000FF', '#0000FF', '#0000FF',
+            '#800080', '#800080', '#800080', '#800080', '#800080', '#800080')
+
+res.all <- NULL
+for(j in 1:39){
+    res <- NULL
+    for(i in 1:39) {
+        tmp <- length(intersect(which(clusters == i), which(reference == j)))
+        res <- c(res, tmp)
+    }
+    res.all <- rbind(res.all, res)
+}
+
+colnames(res.all) <- 1:39
+rownames(res.all) <- 1:39
+
+res <- melt(res.all)
+res <- res[res$value != 0, ]
+
+maxs <- res %>%
+    group_by(Var1) %>%
+    dplyr::summarise(max = max(value))
+
+res <- merge(res, maxs)
+maxs <- res[res$value == res$max, ]
+res <- res[res$value != res$max, ]
+
+res <- rbind(maxs, res)
+res <- res[,1:3]
+
+# remove cycles from the data
+res[, 1] <- paste0(res[, 1], " ")
+res[, 2] <- paste0(" ", res[, 2])
+
+colnames(res) <- c("From", "To", "Weight")
+
+if(!is.null(colors)) {
+    colors <- paste(colors, collapse = "', '")
+    colors <- paste0("['", colors, "']")
+}
+
+Sankey <- gvisSankey(
+    res,
+    from="From",
+    to="To",
+    weight="Weight",
+    options = list(
+        width = 700,
+        height = 1000,
+        sankey = paste0("{
+            node:{
+                label:{
+                    fontName:'Arial',
+                    fontSize:11,color:
+                    '#000000',
+                    bold:true,
+                    italic:false
+                },
+                colors:'#FFFFFF',
+                nodePadding:12
+            },", if(!is.null(colors)) {
+                paste0("link:{
+                colorMode: 'source',
+                colors: ", colors, "
+            },")},
+                "iterations:0
+        }"
+        ))
+)
+
+plot(Sankey)
+

data/S5a.csv

@@ -0,0 +1,199 @@
+variable,value
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