class 17

library(tximport)

folders <- dir(pattern="SRR21568*")
samples <- sub("_quant", "", folders)
files <- file.path( folders, "abundance.h5" )
names(files) <- samples

txi.kallisto <- tximport(files, type = "kallisto", txOut = TRUE)

1 2 3 4 

head(txi.kallisto$counts)

                SRR2156848 SRR2156849 SRR2156850 SRR2156851
ENST00000539570          0          0    0.00000          0
ENST00000576455          0          0    2.62037          0
ENST00000510508          0          0    0.00000          0
ENST00000474471          1          1    1.00000          0
ENST00000381700          0          0    0.00000          0
ENST00000445946          0          0    0.00000          0

colSums(txi.kallisto$counts)

SRR2156848 SRR2156849 SRR2156850 SRR2156851 
    586450    2600800    2372309    2111474 

sum(rowSums(txi.kallisto$counts)>0)

[1] 94657

to.keep <- rowSums(txi.kallisto$counts) > 0
kset.nonzero <- txi.kallisto$counts[to.keep,]

keep2 <- apply(kset.nonzero,1,sd)>0
x <- kset.nonzero[keep2,]

pca <- prcomp(t(x), scale=TRUE)
summary(pca)

Importance of components:
                            PC1      PC2      PC3     PC4
Standard deviation     201.1698 168.6387 160.4157 0.70709
Proportion of Variance   0.4276   0.3005   0.2719 0.00001
Cumulative Proportion    0.4276   0.7281   1.0000 1.00000

plot(pca$x[,1], pca$x[,2],
     col=c("blue","blue","red","red"),
     xlab="PC1", ylab="PC2", pch=16)

plot(pca$x[,1], pca$x[,3],
     col=c("blue","blue","red","red"),
     xlab="PC1", ylab="PC3", pch=16)

plot(pca$x[,2], pca$x[,3],
     col=c("blue","blue","red","red"),
     xlab="PC2", ylab="PC3", pch=16)

library(ggplot2)
library(ggrepel)

mycols <- c("blue","blue","red","red")

ggplot(pca$x) +
  aes(PC1, PC2, label=rownames(pca$x)) +
  geom_point( col=mycols ) +
  geom_text_repel( col=mycols ) +
  theme_bw()

ggplot(pca$x) +
  aes(PC1, PC3, label=rownames(pca$x)) +
  geom_point(col=mycols) +
  geom_text_repel(col=mycols) +
  theme_bw()

ggplot(pca$x) +
  aes(PC2, PC3, label=rownames(pca$x)) +
  geom_point(col=mycols) +
  geom_text_repel(col=mycols) +
  theme_bw()