Last updated: 2023-07-26
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Knit directory: HenriqueDGen/
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File | Version | Author | Date | Message |
---|---|---|---|---|
Rmd | e08b1a6 | LucianoRogerio | 2022-04-05 | Last Analysis |
html | e08b1a6 | LucianoRogerio | 2022-04-05 | Last Analysis |
Rmd | e020351 | LucianoRogerio | 2022-03-29 | Update Henrique Analysis |
html | e020351 | LucianoRogerio | 2022-03-29 | Update Henrique Analysis |
Rmd | 67d31e9 | LucianoRogerio | 2021-12-07 | Fix the navigation buttons on Dendrogram and SH webpage |
html | 67d31e9 | LucianoRogerio | 2021-12-07 | Fix the navigation buttons on Dendrogram and SH webpage |
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 |
library(devtools)
Loading required package: usethis
suppressMessages(library(tidyverse)); suppressMessages(library(circlize))
suppressMessages(library(ComplexHeatmap)); suppressMessages(library(dendextend))
DAPCHenGraph <- readRDS(here::here("output", "DAPCAn.RDS"))
DAPCS <- DAPCHenGraph$ind.coord
DAPCS <- scale(DAPCS, center = T, scale = T)
BLUPS <- readRDS(here::here("output", "BLUPsDiseaseAgro.RDS"))
BLUPS[ , -1] <- scale(BLUPS[ , -1], center = T, scale = T)
BLUPS[is.na(BLUPS)] <- 0
rownames(BLUPS) <- BLUPS$CLONE
col_fun1 = colorRamp2(c(-5.5, 0, 6.5), c("darkblue", "white", "darkred"))
km <- DAPCHenGraph$grp
km1 <- km[km == 1] %>% names
km2 <- km[km == 2] %>% names
km3 <- km[km == 3] %>% names
orderDen1 <- as.dendrogram(hclust(dist(DAPCS[(rownames(DAPCS) %in% km1),1:2]))) %>% order.dendrogram(.) %>%
rownames(DAPCS[(rownames(DAPCS) %in% km1),])[.]
orderDen2 <- as.dendrogram(hclust(dist(DAPCS[(rownames(DAPCS) %in% km2),1:2]))) %>% order.dendrogram(.) %>%
rownames(DAPCS[(rownames(DAPCS) %in% km2),])[.]
orderDen3 <- as.dendrogram(hclust(dist(DAPCS[(rownames(DAPCS) %in% km3),1:2]))) %>% order.dendrogram(.) %>%
rownames(DAPCS[(rownames(DAPCS) %in% km3),])[.]
orderDen <- c(orderDen1, orderDen2, orderDen3)
pos <- match(orderDen, BLUPS$CLONE)
BLUPS <- BLUPS[pos,]
#tiff(filename = here::here("output", "Fig10_CircularHeatmapDAGrp.tiff"), res = 350, compression = "lzw",
# units = "cm", height = 15, width = 15)
set.seed(1)
circos.par(gap.after = c(20))
circos.heatmap(DAPCS[,1:2], col = col_fun1, track.height = 0.1,
dend.side = "outside", clustering.method = "ward.D2", split = km,
dend.track.height = 0.2, show.sector.labels = T)
Note: 1 point is out of plotting region in sector '1', track '1'.
Note: 1 point is out of plotting region in sector '1', track '1'.
Note: 1 point is out of plotting region in sector '1', track '1'.
Note: 1 point is out of plotting region in sector '2', track '1'.
Note: 1 point is out of plotting region in sector '2', track '1'.
Note: 1 point is out of plotting region in sector '2', track '1'.
Note: 1 point is out of plotting region in sector '3', track '1'.
Note: 1 point is out of plotting region in sector '3', track '1'.
Note: 1 point is out of plotting region in sector '3', track '1'.
circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
if(CELL_META$sector.numeric.index == 1) { # the last sector
cn = c("2ºDA", "1ºDA")
n = length(cn)
circos.text(x = rep(-3, n), y = (1:n)*4 - 10.5, labels = cn,
cex = 0.5, adj = c(0, 0.5), facing = "outside")
}
}, bg.border = NA)
Note: 2 points are out of plotting region in sector '1', track '1'.
circos.heatmap(BLUPS[,-1], col = col_fun1, track.height = 0.4, cluster = FALSE)
circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
if(CELL_META$sector.numeric.index == 1) { # the last sector
cn = colnames(BLUPS)[10:2]
n = length(cn)
circos.text(x = rep(-3, n), y = (1:n)*1.15 -0.6, labels = cn,
cex = 0.5, adj = c(0, 0.5), facing = "outside")
}
}, bg.border = NA)
Note: 9 points are out of plotting region in sector '1', track '3'.
circos.clear()
#adding legend key
library(ComplexHeatmap)
lgd_links = Legend(at=c(-5.5,0,6.5), col_fun = col_fun1,
title_position = "topleft", title = "Value", direction = "vertical")
draw(lgd_links, x = unit(1, "npc") - unit(5, "mm"), y = unit(8, "mm"),
just = c("right", "bottom"))
#dev.off()
suppressMessages(library(tidyverse)); library(magrittr)
Attaching package: 'magrittr'
The following object is masked from 'package:purrr':
set_names
The following object is masked from 'package:tidyr':
extract
library(here)
here() starts at /Users/luciano/Documents/GitHub/HenriqueDGen
source(here::here("code", "Shannon-Weaver.R"))
BLUPS <- readRDS(here::here("output", "BLUPsDiseaseAgro.RDS"))
Grps <- readRDS(here::here("output", "DAPCAn.RDS")) %$% grp
Groups <- tibble(CLONE = names(Grps),
Group = as.character(Grps))
BLUPS2 <- BLUPS %>% left_join(Groups, by = "CLONE")
MIN <- apply(BLUPS[,2:10], FUN = min, MARGIN = 2, na.rm = T)
MAX <- apply(BLUPS[,2:10], FUN = max, MARGIN = 2, na.rm = T)
IndSH <- BLUPS2 %>% dplyr::group_by(Group) %>%
dplyr::summarise(SH_Anth = Shannon.Weaver.QT(Anth, min = MIN[1], max = MAX[1],formula = 2),
SH_BlLS = Shannon.Weaver.QT(BlLS, min = MIN[2], max = MAX[2],formula = 2),
SH_BrLS = Shannon.Weaver.QT(BrLS, min = MIN[3], max = MAX[3],formula = 2),
SH_WhLS = Shannon.Weaver.QT(WhLS, min = MIN[4], max = MAX[4],formula = 2),
SH_Vigor = Shannon.Weaver.QT(Vigor, min = MIN[5], max = MAX[5],formula = 2),
SH_NR = Shannon.Weaver.QT(NR, min = MIN[6], max = MAX[6],formula = 2),
SH_DRY = Shannon.Weaver.QT(DRY, min = MIN[7], max = MAX[7],formula = 2),
SH_DMC = Shannon.Weaver.QT(DMC, min = MIN[8], max = MAX[8],formula = 2),
SH_PTR = Shannon.Weaver.QT(PTR, min = MIN[9], max = MAX[9],formula = 2),
SH_PPA = Shannon.Weaver.QT(PPA, min = MIN[10], max = MAX[10],formula = 2))
[Next page]
sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Sao_Paulo
tzcode source: internal
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] reactable_0.4.4 here_1.0.1 magrittr_2.0.3
[4] dendextend_1.17.1 ComplexHeatmap_2.16.0 circlize_0.4.15
[7] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[10] dplyr_1.1.2 purrr_1.0.1 readr_2.1.4
[13] tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2
[16] tidyverse_2.0.0 devtools_2.4.5 usethis_2.2.2
loaded via a namespace (and not attached):
[1] tidyselect_1.2.0 viridisLite_0.4.2 viridis_0.6.4
[4] fastmap_1.1.1 promises_1.2.0.1 digest_0.6.33
[7] timechange_0.2.0 mime_0.12 lifecycle_1.0.3
[10] cluster_2.1.4 ellipsis_0.3.2 processx_3.8.2
[13] compiler_4.3.1 rlang_1.1.1 sass_0.4.7
[16] tools_4.3.1 utf8_1.2.3 yaml_2.3.7
[19] knitr_1.43 prettyunits_1.1.1 htmlwidgets_1.6.2
[22] pkgbuild_1.4.2 RColorBrewer_1.1-3 pkgload_1.3.2.1
[25] miniUI_0.1.1.1 workflowr_1.7.0 withr_2.5.0
[28] BiocGenerics_0.46.0 stats4_4.3.1 fansi_1.0.4
[31] urlchecker_1.0.1 git2r_0.32.0 profvis_0.3.8
[34] xtable_1.8-4 colorspace_2.1-0 scales_1.2.1
[37] iterators_1.0.14 cli_3.6.1 rmarkdown_2.23
[40] crayon_1.5.2 generics_0.1.3 remotes_2.4.2.1
[43] rstudioapi_0.15.0 tzdb_0.4.0 rjson_0.2.21
[46] sessioninfo_1.2.2 cachem_1.0.8 parallel_4.3.1
[49] matrixStats_1.0.0 vctrs_0.6.3 jsonlite_1.8.7
[52] callr_3.7.3 IRanges_2.34.1 hms_1.1.3
[55] GetoptLong_1.0.5 S4Vectors_0.38.1 clue_0.3-64
[58] foreach_1.5.2 jquerylib_0.1.4 glue_1.6.2
[61] reactR_0.4.4 codetools_0.2-19 ps_1.7.5
[64] stringi_1.7.12 gtable_0.3.3 shape_1.4.6
[67] later_1.3.1 munsell_0.5.0 pillar_1.9.0
[70] htmltools_0.5.5 R6_2.5.1 doParallel_1.0.17
[73] rprojroot_2.0.3 evaluate_0.21 shiny_1.7.4.1
[76] highr_0.10 png_0.1-8 memoise_2.0.1
[79] httpuv_1.6.11 bslib_0.5.0 Rcpp_1.0.11
[82] gridExtra_2.3 whisker_0.4.1 xfun_0.39
[85] fs_1.6.3 pkgconfig_2.0.3 GlobalOptions_0.1.2