annotate 04_pca_plot.Rmd @ 2:ab8d558ea6e6 draft default tip

planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 13:57:07 -0500
parents 32210899a3dd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
1 ---
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
2 title: 'Principle component analysis plot'
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
3 output:
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
4 html_document:
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
5 highlight: pygments
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
6 ---
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
7
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
9 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
10 ```
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
11
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
12
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
13 ```{r}
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
14 vsd <- vst(dds, blind=FALSE)
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
15 p = plotPCA(vsd, intgroup=c(opt$X_D)) +
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
16 scale_color_discrete(name = 'Group') +
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
17 theme_classic()
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
18 ggplotly(p)
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
19 ```
32210899a3dd planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
20