Dendrograma e Indice de Shannon-Weaver
LucianoRogerio e HenriqueBernardino
2021-11-09
Last updated: 2021-12-07
Checks: 6 1
Knit directory: HenriqueDGen/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 2abb2a7 | LucianoRogerio | 2021-12-07 | Small english changes at the website |
| html | 2abb2a7 | LucianoRogerio | 2021-12-07 | Small english changes at the website |
| Rmd | f272038 | LucianoRogerio | 2021-12-07 | Update of the analysis and website layout |
| html | f272038 | LucianoRogerio | 2021-12-07 | Update of the analysis and website layout |
| Rmd | e535227 | LucianoRogerio | 2021-11-24 | Update Layout Website |
| html | 3ca0498 | LucianoRogerio | 2021-11-18 | Build site. |
| Rmd | f51cdc6 | LucianoRogerio | 2021-11-18 | Add the Dendrogram analysis |
| html | f51cdc6 | LucianoRogerio | 2021-11-18 | Add the Dendrogram analysis |
| Rmd | cbf63bd | LucianoRogerio | 2021-11-16 | Add Dendrogram |
| html | cbf63bd | LucianoRogerio | 2021-11-16 | Add Dendrogram |
| Rmd | e89306d | LucianoRogerio | 2021-11-09 | DAPC Analysis finished |
| Rmd | 33422ee | LucianoRogerio | 2021-11-09 | DAPC Analysis finished |
Dendrogram
library(devtools)Loading required package: usethis#install_version("circlize", version = "0.4.10", repos = "http://cran.us.r-project.org")
suppressMessages(library(tidyverse)); suppressMessages(library(circlize))
suppressMessages(library(ComplexHeatmap)); suppressMessages(library(dendextend))
DAPCHenGraph <- readRDS(here::here("output", "DAPCAn.RDS"))
DAPCS <- DAPCHenGraph$ind.coord
DAPCS <- scale(DAPCS, center = T, scale = T)
BLUPS <- readRDS(here::here("output", "BLUPsDisease.RDS"))
BLUPS[ , 2:6] <- scale(BLUPS[ , 2:6], center = T, scale = T)
BLUPS[is.na(BLUPS)] <- 0
rownames(BLUPS) <- BLUPS$CLONE
col_fun1 = colorRamp2(c(-3.3, 0, 4.8), c("darkblue", "white", "darkred"))
col_fun2 = colorRamp2(c(-3.5, 0, 6.5), c("darkblue", "white", "darkred"))
set.seed(1)
circos.par(gap.after = c(25))
circos.heatmap(DAPCS, col = col_fun1, track.height = 0.15,
dend.side = "outside", clustering.method = "ward.D2",
dend.callback = function(dend, m, si) {
color_branches(dend, k = 4, col = 1:4)
},
dend.track.height = 0.3)
circos.heatmap(BLUPS[,2:6], col = col_fun2, track.height = 0.3)
circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
if(CELL_META$sector.numeric.index == 1) { # the last sector
cn = colnames(BLUPS)[6:2]
n = length(cn)
circos.text(x = rep(0.04, n), y = (1:n) -0.6, labels = cn,
cex = 0.5, adj = c(0, 0.5), facing = "outside")
}
}, bg.border = NA)
circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
if(CELL_META$sector.numeric.index == 1) { # the last sector
cn = c("2ºDA", "1ºDA")
n = length(cn)
circos.text(x = rep(0.04, n), y = (1:n) + 5, labels = cn,
cex = 0.5, adj = c(0, 0.5), facing = "outside")
}
}, bg.border = NA)Note: 2 points are out of plotting region in sector 'group', track '3'.circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
circos.text(c(670, 430, 250, 90), c(11, 10, 11, 11) + convert_y(2, "mm"),
paste0("group ", c(1:4)),
facing = "bending.inside", cex = 0.8,
adj = c(0.5, 0), niceFacing = TRUE)
}, bg.border = NA)Note: 4 points are out of plotting region in sector 'group', track '3'.Note: 1 point is out of plotting region in sector 'group', track '3'.Note: 7 points are out of plotting region in sector 'group', track '3'.Note: 3 points are out of plotting region in sector 'group', track '3'.Note: 7 points are out of plotting region in sector 'group', track '3'.
Note: 7 points are out of plotting region in sector 'group', track '3'.
Note: 7 points are out of plotting region in sector 'group', track '3'.
| Version | Author | Date |
|---|---|---|
| cbf63bd | LucianoRogerio | 2021-11-16 |
circos.clear()[Next page]
sessionInfo()R version 4.1.1 (2021-08-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.6.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] dendextend_1.15.2 ComplexHeatmap_2.10.0 circlize_0.4.13
[4] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
[7] purrr_0.3.4 readr_2.1.0 tidyr_1.1.4
[10] tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1
[13] devtools_2.4.2 usethis_2.1.3
loaded via a namespace (and not attached):
[1] matrixStats_0.61.0 fs_1.5.0 lubridate_1.8.0
[4] RColorBrewer_1.1-2 doParallel_1.0.16 httr_1.4.2
[7] rprojroot_2.0.2 tools_4.1.1 backports_1.3.0
[10] bslib_0.3.1 utf8_1.2.2 R6_2.5.1
[13] BiocGenerics_0.40.0 DBI_1.1.1 colorspace_2.0-2
[16] GetoptLong_1.0.5 withr_2.4.2 gridExtra_2.3
[19] tidyselect_1.1.1 prettyunits_1.1.1 processx_3.5.2
[22] compiler_4.1.1 git2r_0.29.0 cli_3.1.0
[25] rvest_1.0.2 xml2_1.3.2 desc_1.4.0
[28] sass_0.4.0 scales_1.1.1 callr_3.7.0
[31] digest_0.6.28 rmarkdown_2.11 pkgconfig_2.0.3
[34] htmltools_0.5.2 sessioninfo_1.2.1 highr_0.9
[37] dbplyr_2.1.1 fastmap_1.1.0 rlang_0.4.12
[40] GlobalOptions_0.1.2 readxl_1.3.1 rstudioapi_0.13
[43] shape_1.4.6 jquerylib_0.1.4 generics_0.1.1
[46] jsonlite_1.7.2 magrittr_2.0.1 S4Vectors_0.32.2
[49] Rcpp_1.0.7 munsell_0.5.0 fansi_0.5.0
[52] viridis_0.6.2 lifecycle_1.0.1 stringi_1.7.5
[55] whisker_0.4 yaml_2.2.1 pkgbuild_1.2.0
[58] parallel_4.1.1 promises_1.2.0.1 crayon_1.4.2
[61] haven_2.4.3 hms_1.1.1 knitr_1.36
[64] ps_1.6.0 pillar_1.6.4 rjson_0.2.20
[67] stats4_4.1.1 codetools_0.2-18 pkgload_1.2.3
[70] reprex_2.0.1 glue_1.5.0 evaluate_0.14
[73] remotes_2.4.1 modelr_0.1.8 png_0.1-7
[76] foreach_1.5.1 vctrs_0.3.8 tzdb_0.2.0
[79] httpuv_1.6.3 testthat_3.1.0 cellranger_1.1.0
[82] gtable_0.3.0 clue_0.3-60 assertthat_0.2.1
[85] cachem_1.0.6 xfun_0.28 broom_0.7.10
[88] later_1.3.0 viridisLite_0.4.0 iterators_1.0.13
[91] IRanges_2.28.0 memoise_2.0.0 cluster_2.1.2
[94] workflowr_1.6.2 ellipsis_0.3.2 here_1.0.1