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annotate render_tree.R @ 0:342fe8c2d8bb draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
author dfornika
date Sat, 29 Jun 2019 00:13:08 -0400
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children 9f0241ee55e8
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342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
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diff changeset
1 #!/usr/bin/env Rscript
342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
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342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
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3 suppressMessages(
342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
parents:
diff changeset
4 library(ggtree)
342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
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5 )
342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
parents:
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6
342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
parents:
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7 args = commandArgs(trailingOnly=TRUE)
342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
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342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
parents:
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9 tree <- read.tree(args[1])
342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
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342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
parents:
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11 tree_plot <- ggplot(tree, aes(x, y)) +
342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
parents:
diff changeset
12 geom_tree() +
342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
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13 theme_tree2() +
342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
parents:
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14 geom_tiplab()
342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
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342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
parents:
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16 suppressMessages(
342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
parents:
diff changeset
17 ggsave(args[2], plot=tree_plot, device="png")
342fe8c2d8bb planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
dfornika
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18 )