Messy tSNE code

Sponge tSNE.R

spongeSmallIn <- readRDS("data/spongeSmall.rds")
spongeSmall <- MALDIquant::intensityMatrix(spongeSmallIn)
spongeSmall[is.na(spongeSmall)] <- 0.000000001
spongeSmall <- prcomp(log10(spongeSmall))
spongeSmall <- spongeSmall$x[,1:50]
z <- sapply(spongeSmallIn, function(x) x@metaData$Strain )
q <- as.data.frame(spongeSmall)
rownames(q) <- z


z1 <- Rtsne::Rtsne(q, pca=FALSE, dims=3, perplexity = 10, theta = 0, max_iter = 1000,check_duplicates=FALSE)


d <-z1
d <- as.data.frame(d$Y)
colnames(d) <- c("Dim.1","Dim.2","Dim.3")
d <-  as.data.frame(d)

pcaDat <- d

plot(pcaDat[,1:2])
    
  mydata <- pcaDat
wss <- (nrow(mydata)-1)*sum(apply(mydata,2,var))
  for (i in 2:15) wss[i] <- sum(kmeans(mydata,
                                       centers=i)$withinss)
plot(1:15, wss, type="b", xlab="Number of Clusters",
     ylab="Within groups sum of squares")
    
    
    


a <- kmeans(pcaDat, 12)


b <- RColorBrewer::brewer.pal(12, "Paired")


pp <- bind_cols(pcaDat, k=as.factor(a$cluster))

colnames(pp) <- c("a1", "b1", "c1", "d1")
pp <- as_tibble(pp)

   plotly::plot_ly(data=pp,x= ~a1, y= ~b1, z = ~c1,
                   type="scatter3d",mode="markers",hoverinfo = 'text',text=rownames(q), color = ~d1, colors = b)