Publications by R on Guangchuang Yu
Edge coloring with user data
Coloring edges in ggtree is quite easy, as we can map the color to numerical or categorical values via the aes(color=VAR) syntax. For user’s own data, it is also easy as ggtree provide the %<+% operator to attach user data. But as it seems not so obviously for ggtree users, see question 1, 2, and 3, I will demonstrate how to color edges using u...
1447 sym R (599 sym/3 pcs) 4 img
Edge coloring with user data
Coloring edges in ggtree is quite easy, as we can map the color to numerical or categorical values via the aes(color=VAR) syntax. For user’s own data, it is also easy as ggtree provide the %<+% operator to attach user data. But as it seems not so obviously for ggtree users, see question 1, 2, and 3, I will demonstrate how to color edges using u...
1206 sym R (599 sym/3 pcs) 4 img
ggtree version of plotTree
PLOTTING TREES + DATA is difficult. @DrKatHolt developed plotTree (R and Python scripts) to visualize associated data with trees, e.g. heatmap, horizontal bar etc. I reproduced the examples presented in the plotTree repo using ggtree. Source code is freely available in https://github.com/GuangchuangYu/plotTree-ggtree. Here are the outputs produce...
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ggtree version of plotTree
PLOTTING TREES + DATA is difficult. @DrKatHolt developed plotTree (R and Python scripts) to visualize associated data with trees, e.g. heatmap, horizontal bar etc. I reproduced the examples presented in the plotTree repo using ggtree. Source code is freely available in https://github.com/GuangchuangYu/plotTree-ggtree. Here are the outputs produce...
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add layer to specific panel of facet_plot output
This is a question from ggtree google group: Dear ggtree team, how can I apply a geom_xxx to only one facet panel? For example if i want to get geom_hline(yintersect=1:30) or a geom_text() in the dot panel? I cant see the facet_grid(. ~ var) function call, so I don’t know which subsetting to use. I have already read http://stackoverflow.com/qu...
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add layer to specific panel of facet_plot output
This is a question from ggtree google group: Dear ggtree team, how can I apply a geom_xxx to only one facet panel? For example if i want to get geom_hline(yintersect=1:30) or a geom_text() in the dot panel? I cant see the facet_grid(. ~ var) function call, so I don’t know which subsetting to use. I have already read http://stackoverflow.com/qu...
1801 sym R (1189 sym/3 pcs) 4 img
dotplot for GSEA result
For GSEA analysis, we are familar with the above figure which shows the running enrichment score. But for most of the software, it lack of visualization method to summarize the whole enrichment result. In DOSE (and related tools including clusterProfiler, ReactomePA and meshes), we provide enrichMap and cnetplot to summarize GSEA result. Here is...
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dotplot for GSEA result
For GSEA analysis, we are familar with the above figure which shows the running enrichment score. But for most of the software, it lack of visualization method to summarize the whole enrichment result. In DOSE (and related tools including clusterProfiler, ReactomePA and meshes), we provide enrichMap and cnetplot to summarize GSEA result. Here is...
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convert graphic object to tree object using treeio
I have splitted ggtree to 2 packages, treeio and ggtree. Now ggtree is mainly focus on visualization and annotation, while treeio focus on parsing and exporting tree files. Here is a welcome message from treeio that you can convert ggtree output to tree object which can be exported as newick or nexus file if you want. Thanks to ggplot2, output of...
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convert graphic object to tree object using treeio
I have splitted ggtree to 2 packages, treeio and ggtree. Now ggtree is mainly focus on visualization and annotation, while treeio focus on parsing and exporting tree files. Here is a welcome message from treeio that you can convert ggtree output to tree object which can be exported as newick or nexus file if you want. Thanks to ggplot2, output of...
2738 sym R (294 sym/2 pcs) 2 img