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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 13:57:07 -0500
parents 32210899a3dd
children
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1 ---
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2 title: 'MA-plot'
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3 output:
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4 html_document:
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5 highlight: pygments
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6 ---
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8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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9 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
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10 ```
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13 ```{r warning=FALSE}
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14 log_fold_change = res$log2FoldChange
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15 base_mean = res$baseMean
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16 significant = res$padj
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17 significant[significant < 0.1] = 'yes'
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18 significant[significant != 'yes'] = 'no'
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20 maplot_df = data.frame(log_fold_change, base_mean, significant)
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21 maplot_df = maplot_df[!is.na(maplot_df$significant), ]
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22 p = ggplot(data = maplot_df) +
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23 geom_point(mapping = aes(log(base_mean), log_fold_change, color = significant),
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24 size = 0.5) +
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25 scale_color_manual(name = 'Significant',
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26 values = c('no' = 'black', 'yes' = 'red'),
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27 labels = c('No', 'Yes')) +
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28 xlab('Log base mean') +
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29 ylab('Log fold change') +
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30 theme_classic()
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32 plotly::ggplotly(p)
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33 ```