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20 hours ago •
YuLab-SMU
YuLab-SMU
geom_hilight with gradient does not show anything
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Using the example code in the help for geom_hilight() does not result in gradient rectangles.
library(ggtree)
#> ggtree v3.3.1 For help: https://yulab-smu.top/treedata-book/
#>
#> If you use ggtree in published research, please cite the most appropriate paper(s):
#>
#> 1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96
#> 2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution. 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
#> 3. Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
set.seed(102)
tree <- rtree(60)
p <- ggtree(tree)
p1 <- p + geom_hilight(node=62) + geom_hilight(node=88, fill="red")
p1
dat <- data.frame(id=c(62, 88), type=c("A", "B"))
p2 <- p + geom_hilight(data=dat, mapping=aes(node=id, fill=type))
p2
# display the high light layer with gradiental color rectangular.
p6 <- p + geom_hilight(data=dat, mapping=aes(node=id, fill=type), type = "gradient", alpha=0.68)
p6
p7 <- p + geom_hilight(data=dat, mapping=aes(node=id, fill=type), type = "gradient", gradient.direction="tr", alpha=0.68)
p7
Created on 2022-02-02 by the reprex package (v2.0.1)
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
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#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Asia/Tokyo
#> date 2022-02-02
#> pandoc 2.11.4 @ /Applications/RStudio.app/Contents/MacOS/pandoc/ (via rmarkdown)
#>
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Hi,
Thanks for the reprex.
Use the parameter gradient =TRUE instead of type ='gradient'. The type option is used for the tree layout
p+ geom_hilight(data=dat, aes(node=id, fill=type),extend=1 , gradient = TRUE)
I am in Package ggtree version 3.1.5.900 and the manual of the function is clear to me. Does it answer your question ?
Hi,
Thanks for the reprex.
Use the parameter gradient =TRUE instead of type ='gradient'. The type option is used for the tree layout
p+ geom_hilight(data=dat, aes(node=id, fill=type),extend=1 , gradient = TRUE)
I am in Package ggtree version 3.1.5.900 and the manual of the function is clear to me. Does it answer your question ?
Thanks for the quick reply. That doesn't seem to work for me. Perhaps it is because you are using an older version (3.1.5.900 vs 3.3.1). If so, it needs to be fixed in the newer version.
library(ggtree)
#> ggtree v3.3.1 For help: https://yulab-smu.top/treedata-book/
#>
#> If you use ggtree in published research, please cite the most appropriate paper(s):
#>
#> 1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96
#> 2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution. 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
#> 3. Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
set.seed(102)
tree <- rtree(60)
p <- ggtree(tree)
dat <- data.frame(id=c(62, 88), type=c("A", "B"))
p + geom_hilight(data=dat, aes(node=id, fill=type),extend=1 , gradient = TRUE)
Created on 2022-02-02 by the reprex package (v2.0.1)
Now, the gradient highlight only can work on the Linux Platform. Or using svg on Windows. You can refer to the answer
