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fullTable_heatmap_internalComparison.R 8.95 KiB
suppressMessages(library(dplyr))
suppressMessages(library(formattable))
fullTableOfStats<-read.table(file = snakemake@input[[1]], sep = "", header = TRUE, row.names=NULL, check.names = FALSE)
fullTableOfStats$Gaps_per_Gb <- ((fullTableOfStats$Gaps * fullTableOfStats$Est_Size_Mb)/1000)
fullTableOfStats$Gaps_per_Gb <- as.integer(fullTableOfStats$Gaps_per_Gb)
selectionOfStats_internalComparisonHeatmap <- fullTableOfStats %>%
select(c('ASM_ID','ASM_LEVEL', 'Bases_Mb', 'Het_%','GC_%', 'Gaps_per_Gb', 'Scaff', 'Cont',
'Longest_Scaff_Mb','Scaff_NG50_Mb', 'Scaff_NG95_Mb',
'Longest_Cont_Mb', 'Cont_NG50_Mb','Cont_NG95_Mb',
'QV', 'Completeness',
'Comp_BUSCOs_%','Comp_Single_BUSCOs_%'))
customBlue_max = "#2e96ff"
customBlue_min = "#dcecfc"
customGray_max = "#8c8c8c"
customGray_min = "#e6e6e6"
sink(file = snakemake@output[[1]])
format_table(selectionOfStats_internalComparisonHeatmap,
align =c("l","c","c","c","c", "c", "c", "c", "c"),
list(Bases_Mb = color_tile(customGray_min, customGray_max),
`Het_%` = color_tile(customGray_min, customGray_max),
`GC_%` = color_tile(customGray_min, customGray_max),
Gaps_per_Gb = color_tile(customBlue_max, customBlue_min),
Scaff = color_tile(customBlue_max,customBlue_min),
Cont = color_tile(customBlue_max,customBlue_min),
Longest_Scaff_Mb = color_tile(customBlue_min, customBlue_max),
Scaff_NG50_Mb = color_tile(customBlue_min, customBlue_max),
Scaff_NG95_Mb = color_tile(customBlue_min, customBlue_max),
Longest_Cont_Mb = color_tile(customBlue_min, customBlue_max),
Cont_NG50_Mb = color_tile(customBlue_min, customBlue_max),
Cont_NG95_Mb = color_tile(customBlue_min, customBlue_max),
QV = color_tile(customBlue_min, customBlue_max),
Completeness = color_tile(customBlue_min, customBlue_max),
`Comp_BUSCOs_%` = color_tile(customBlue_min, customBlue_max),
`Comp_Single_BUSCOs_%` = color_tile(customBlue_min, customBlue_max)))
cat('<br>')
cat("\n")
cat('<br>')
legendTable<-read.table(file = snakemake@params[[1]], sep = "", header = TRUE, row.names=NULL, check.names = FALSE)
format_table(legendTable,
align =c("c","c","c", "c", "c", "c", "c","c","c","c", "c", "c", "c", "c","c", "c"),
list(Bases_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Bases_Mb == 'Max',customGray_max, customGray_min))),
`Het_%` = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(`Het_%` == 'Max',customGray_max, customGray_min))),
`GC_%` = formatter("span",
style = ~style(display = "block", padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(`GC_%` == 'Max',customGray_max, customGray_min))),
Gaps_per_Gb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Gaps_per_Gb == 'Min',customBlue_max, customBlue_min))),
Scaff = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Scaff == 'Min',customBlue_max, customBlue_min))),
Cont = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Cont == 'Min',customBlue_max, customBlue_min))),
Longest_Scaff_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Longest_Scaff_Mb == 'Max',customBlue_max, customBlue_min))),
Scaff_NG50_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Scaff_NG50_Mb == 'Max',customBlue_max, customBlue_min))),
Scaff_NG95_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Scaff_NG95_Mb == 'Max',customBlue_max, customBlue_min))),
Longest_Cont_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Longest_Cont_Mb == 'Max',customBlue_max, customBlue_min))),
Cont_NG50_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Cont_NG50_Mb == 'Max',customBlue_max, customBlue_min))),
Cont_NG95_Mb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Cont_NG95_Mb == 'Max',customBlue_max, customBlue_min))),
QV = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(QV == 'Max',customBlue_max, customBlue_min))),
Completeness = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(Completeness == 'Max',customBlue_max, customBlue_min))),
`Comp_BUSCOs_%` = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(`Comp_BUSCOs_%` == 'Max',customBlue_max, customBlue_min))),
`Comp_Single_BUSCOs_%` = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(`Comp_Single_BUSCOs_%` == 'Max',customBlue_max, customBlue_min)))))
sink(file = NULL)