Last updated: 2023-10-03

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File Version Author Date Message
Rmd 54268fe LucianoRogerio 2023-07-31 Adding Foliar Retention to final Boxplot
Rmd fef5cf2 LucianoRogerio 2023-07-26 Adicao Dados 2022
html fef5cf2 LucianoRogerio 2023-07-26 Adicao Dados 2022
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

Dendrogram

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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"))

Version Author Date
fef5cf2 LucianoRogerio 2023-07-26
e08b1a6 LucianoRogerio 2022-04-05
e020351 LucianoRogerio 2022-03-29 
#dev.off()

Shannon-Weaver index

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[,2:11], FUN = min, MARGIN = 2, na.rm = T)
MAX <- apply(BLUPS[,2:11], 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_RF = Shannon.Weaver.QT(RF, min = MIN[7], max = MAX[7],formula = 2),
                   SH_DRY = Shannon.Weaver.QT(DRY, min = MIN[8], max = MAX[8],formula = 2),
                   SH_DMC = Shannon.Weaver.QT(DMC, min = MIN[9], max = MAX[9],formula = 2),
                   SH_PTR = Shannon.Weaver.QT(PTR, min = MIN[10], max = MAX[10],formula = 2),
                   SH_PPA = Shannon.Weaver.QT(PPA, min = MIN[11], max = MAX[11],formula = 2))

Table 1. Shannon-Weaver Index per DAPC group of cassava agronomic and foliar disease traits

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sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.5.2

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_1.0.2           readr_2.1.4          
[13] tidyr_1.3.0           tibble_3.2.1          ggplot2_3.4.3        
[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_1.2.1      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_2.24     
[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] crosstalk_1.2.0     foreach_1.5.2       jquerylib_0.1.4    
[61] glue_1.6.2          reactR_0.4.4        codetools_0.2-19   
[64] ps_1.7.5            stringi_1.7.12      gtable_0.3.3       
[67] shape_1.4.6         later_1.3.1         munsell_0.5.0      
[70] pillar_1.9.0        htmltools_0.5.6     R6_2.5.1           
[73] doParallel_1.0.17   rprojroot_2.0.3     evaluate_0.21      
[76] shiny_1.7.5         highr_0.10          png_0.1-8          
[79] memoise_2.0.1       httpuv_1.6.11       bslib_0.5.1        
[82] Rcpp_1.0.11         gridExtra_2.3       whisker_0.4.1      
[85] xfun_0.40           fs_1.6.3            pkgconfig_2.0.3    
[88] GlobalOptions_0.1.2