From b998340763b34c31603c9d4ee5401b9a03d38db9 Mon Sep 17 00:00:00 2001
From: "Hartanto, Margi" <margi.hartanto@wur.nl>
Date: Tue, 18 Feb 2020 17:14:34 +0100
Subject: [PATCH] discriminate parents in PCA plot
---
1-clustering.R | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/1-clustering.R b/1-clustering.R
index ab8a030..7c1ec76 100644
--- a/1-clustering.R
+++ b/1-clustering.R
@@ -70,16 +70,16 @@
pr.out <- prcomp(x = (t(trait.matrix)), center = T, scale. = F)
pc.df <- data.frame(pc1 = pr.out$x[, 1],
pc2 = pr.out$x[, 2],
- stage = sample.stage,
- population = c(rep('parent', 16), rep('RIL', 164)))
+ stage = as.character(sample.stage),
+ population = substring(colnames(trait.matrix), 1, 3))
pc.sum <- summary(pr.out)
pc1.var <- round(pc.sum$importance[2, 'PC1'] * 100, 2)
pc2.var <- round(pc.sum$importance[2, 'PC2'] * 100, 2)
- pca.all <- ggplot(pc.df, aes(x = pc1, y = pc2, color = factor(stage, level = c('pd', 'ar', 'im', 'rp')))) +
+ pca.all <- ggplot(pc.df, aes(x = pc1, y = pc2, color = factor(stage, level = c('parent', 'pd', 'ar', 'im', 'rp')))) +
geom_point(aes(shape = population)) +
scale_colour_manual(values = c('#ccbb44', '#228833', '#4477aa', '#cc3311')) +
- scale_shape_manual(values = c(17, 19)) +
+ scale_shape_manual(values = c(2, 19, 6)) +
labs(x = paste0("PC1 (", pc1.var, "%)"), y = paste0("PC2 (", pc2.var, "%)")) +
labs(colour = 'stage') +
theme(text = element_text(size = 10),
@@ -101,7 +101,7 @@
units = 'px',
res = 300,
compression = 'lzw')
- pca.all
+ print(pca.all)
dev.off()
# PCA per stage ####
--
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