Skip to content
Snippets Groups Projects
Commit 9d91b3aa authored by galeov97's avatar galeov97
Browse files

Update fullTable_heatmap_external_metrics.R

parent 98e86813
Branches
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
scripts/compare_results/fullTable_heatmap_external_metrics.R
+ 144
− 142
View file @ 9d91b3aa
#!/usr/bin/env Rscript
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$Total_bp) *1000000000)
fullTableOfStats$Gaps_per_Gb <- as.integer(fullTableOfStats$Gaps_per_Gb)
customPurple='#c699e8'
customGreen='#8fc773'
selectionOfStats_colouredHeatmap <- fullTableOfStats %>%
select(c('ASM_ID',
'Gaps_per_Gb', 'Scaf_N50',
'Cont_N50','qv',
'Kmer_Compl', "Comp_Single_BUSCOs_%" = BUSCO_S)) %>%
mutate("Comp_Single_BUSCOs_%" = as.numeric(sub("%", "", as.character(`Comp_Single_BUSCOs_%`))))
sink(file = snakemake@output[[1]])
format_table(selectionOfStats_colouredHeatmap,
align =c("l","c","c","c","c", "c", "c", "c", "c"),
list(Gaps_per_Gb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(Gaps_per_Gb,1001, 10000), "#FFCC99",
ifelse(between(Gaps_per_Gb,201 , 1000), customGreen,
ifelse(Gaps_per_Gb <= 200, customPurple, "#FF9999"))))),
Scaf_N50 = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(Scaf_N50,0.1, 9.99999), "#FFCC99",
ifelse(between(Scaf_N50,10, 99.99999), customGreen,
ifelse(Scaf_N50 >= 100, customPurple, "#FF9999"))))),
Scaf_L50 = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(Scaf_L50,0.1, 9.99999), "#FFCC99",
ifelse(between(Scaf_L50,10, 99.99999), customGreen,
ifelse(Scaf_L50 >= 100, customPurple, "#FF9999"))))),
Cont_N50 = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(Cont_N50,0.01, 0.99999), "#FFCC99",
ifelse(between(Cont_N50,1, 9.999999), customGreen,
ifelse(Cont_N50 >= 10, customPurple, "#FF9999"))))),
Kmer_Compl = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(Kmer_Compl,80, 89.9999), "#FFCC99",
ifelse(between(Kmer_Compl,90, 94.99999), customGreen,
ifelse(Kmer_Compl >= 95, customPurple, "#FF9999"))))),
qv = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(qv,35, 39.9999999999), "#FFCC99",
ifelse(between(qv,40, 49.999999999), customGreen,
ifelse(qv >= 50, customPurple, "#FF9999"))))),
`Comp_Single_BUSCOs_%` = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(`Comp_Single_BUSCOs_%`,80, 89.9999), "#FFCC99",
ifelse(between(`Comp_Single_BUSCOs_%`,90, 94.99999), customGreen,
ifelse(`Comp_Single_BUSCOs_%` >= 95, customPurple, "#FF9999")))))))
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"),
list(Gaps_per_Gb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '150px',
`background-color` = ifelse(Gaps_per_Gb == '> 10000',"#FF9999",
ifelse(Gaps_per_Gb == '1000 - 10000',"#FFCC99",
ifelse(Gaps_per_Gb == '200 - 1000',customGreen, customPurple))))),
Scaf_N50 = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '150px',
`background-color` = ifelse(Scaf_N50 == '< 0.1Mbp',"#FF9999",
ifelse(Scaf_N50 == '0.1Mbp - 10Mbp',"#FFCC99",
ifelse(Scaf_N50 == '10Mbp - 100Mbp',customGreen, customPurple))))),
Cont_N50 = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '150px',
`background-color` = ifelse(Cont_N50 == '< 0.01Mbp',"#FF9999",
ifelse(Cont_N50 == '0.01Mbp - 1Mbp',"#FFCC99",
ifelse(Cont_N50 == '1Mbp - 10Mbp',customGreen, customPurple))))),
qv = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '100px',
`background-color` = ifelse(qv == '< 35',"#FF9999",
ifelse(qv == '35 - 40',"#FFCC99",
ifelse(qv == '40 - 50',customGreen, customPurple))))),
Kmer_Compl = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '150px',
`background-color` = ifelse(Kmer_Compl == '< 80%',"#FF9999",
ifelse(Kmer_Compl == '80% - 90%',"#FFCC99",
ifelse(Kmer_Compl == '90% - 95%',customGreen, customPurple))))),
`Comp_Single_BUSCOs_%` = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '220px',
`background-color` = ifelse(`Comp_Single_BUSCOs_%` == '< 80%',"#FF9999",
ifelse(`Comp_Single_BUSCOs_%` == '80% - 90%',"#FFCC99",
ifelse(`Comp_Single_BUSCOs_%` == '90% - 95%',customGreen, customPurple)))))))
sink(file = NULL)
#!/usr/bin/env Rscript
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$Gaps / fullTableOfStats$Total_bp) *1000000000)
fullTableOfStats$Gaps_per_Gb <- as.integer(fullTableOfStats$Gaps_per_Gb)
#customPurple='#c699e8'
#customGreen='#8fc773'
customPurple='#99c1f1'
customGreen='#8ff0a4'
selectionOfStats_colouredHeatmap <- fullTableOfStats %>%
select(c('ASM_ID',
'Gaps_per_Gb', 'Scaf_N50',
'Cont_N50','qv',
'Kmer_Compl', "Comp_Single_BUSCOs_%" = BUSCO_S)) %>%
mutate("Comp_Single_BUSCOs_%" = as.numeric(sub("%", "", as.character(`Comp_Single_BUSCOs_%`))))
sink(file = snakemake@output[[1]])
format_table(selectionOfStats_colouredHeatmap,
align =c("l","c","c","c","c", "c", "c", "c", "c"),
list(Gaps_per_Gb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(Gaps_per_Gb,1001, 10000), "#F9F06B",
ifelse(between(Gaps_per_Gb,201 , 1000), customGreen,
ifelse(Gaps_per_Gb <= 200, customPurple, "#F66151"))))),
Scaf_N50 = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(Scaf_N50,0.1, 9.99999), "#F9F06B",
ifelse(between(Scaf_N50,10, 99.99999), customGreen,
ifelse(Scaf_N50 >= 100, customPurple, "#F66151"))))),
Scaf_L50 = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(Scaf_L50,0.1, 9.99999), "#F9F06B",
ifelse(between(Scaf_L50,10, 99.99999), customGreen,
ifelse(Scaf_L50 >= 100, customPurple, "#F66151"))))),
Cont_N50 = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(Cont_N50,0.01, 0.99999), "#F9F06B",
ifelse(between(Cont_N50,1, 9.999999), customGreen,
ifelse(Cont_N50 >= 10, customPurple, "#F66151"))))),
Kmer_Compl = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(Kmer_Compl,80, 89.9999), "#F9F06B",
ifelse(between(Kmer_Compl,90, 94.99999), customGreen,
ifelse(Kmer_Compl >= 95, customPurple, "#F66151"))))),
qv = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(qv,35, 39.9999999999), "#F9F06B",
ifelse(between(qv,40, 49.999999999), customGreen,
ifelse(qv >= 50, customPurple, "#F66151"))))),
`Comp_Single_BUSCOs_%` = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
`background-color` = ifelse(between(`Comp_Single_BUSCOs_%`,80, 89.9999), "#F9F06B",
ifelse(between(`Comp_Single_BUSCOs_%`,90, 94.99999), customGreen,
ifelse(`Comp_Single_BUSCOs_%` >= 95, customPurple, "#F66151")))))))
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"),
list(Gaps_per_Gb = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '150px',
`background-color` = ifelse(Gaps_per_Gb == '> 10000',"#F66151",
ifelse(Gaps_per_Gb == '1000 - 10000',"#F9F06B",
ifelse(Gaps_per_Gb == '200 - 1000',customGreen, customPurple))))),
Scaf_N50 = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '150px',
`background-color` = ifelse(Scaf_N50 == '< 0.1Mbp',"#F66151",
ifelse(Scaf_N50 == '0.1Mbp - 10Mbp',"#F9F06B",
ifelse(Scaf_N50 == '10Mbp - 100Mbp',customGreen, customPurple))))),
Cont_N50 = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '150px',
`background-color` = ifelse(Cont_N50 == '< 0.01Mbp',"#F66151",
ifelse(Cont_N50 == '0.01Mbp - 1Mbp',"#F9F06B",
ifelse(Cont_N50 == '1Mbp - 10Mbp',customGreen, customPurple))))),
qv = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '100px',
`background-color` = ifelse(qv == '< 35',"#F66151",
ifelse(qv == '35 - 40',"#F9F06B",
ifelse(qv == '40 - 50',customGreen, customPurple))))),
Kmer_Compl = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '150px',
`background-color` = ifelse(Kmer_Compl == '< 80%',"#F66151",
ifelse(Kmer_Compl == '80% - 90%',"#F9F06B",
ifelse(Kmer_Compl == '90% - 95%',customGreen, customPurple))))),
`Comp_Single_BUSCOs_%` = formatter("span",
style = ~style(display = "block",
padding = "0 4px",
`border-radius` = "3px",
"font.size" = "12px",
"width" = '220px',
`background-color` = ifelse(`Comp_Single_BUSCOs_%` == '< 80%',"#F66151",
ifelse(`Comp_Single_BUSCOs_%` == '80% - 90%',"#F9F06B",
ifelse(`Comp_Single_BUSCOs_%` == '90% - 95%',customGreen, customPurple)))))))
sink(file = NULL)
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment