updated assembler names and colors in workflow_report/scripts/utils.R

workflow_report/scripts/utils.R

@@ -397,15 +397,13 @@ DIAMOND_VAR_LABELLER <- function(x){
 ASM_TOOL_NAMES <- c(
     # LR, SR, hybrid
     "flye"="Flye",
+    "wtdbg2"="wtdbg2",
+    "canu"="Canu",
     "megahit"="MEGAHIT",
     "metaspades"="metaSPAdes",
     "operams"="OPERA-MS",
     "metaspadeshybrid"="metaSPAdes (H)",
-    # polishing w/ metaT (w/o LR)
-    "megahitmetatracon"="Racon(MEGAHIT + metaT)",
-    "metaspadesmetatracon"="Racon(metaSPAdes + metaT)",
-    "operamsmetatracon"="Racon(OPERA-MS + metaT)",
-    "metaspadeshybridmetatracon"="Racon(metaSPAdes (H) + metaT)"
+    "imp3"="IMP3 (MG/MT)"
 )
 ASM_TOOL_NAMES <- ASM_TOOL_NAMES[c(
     snakemake@config$assemblers$lr,
@@ -413,34 +411,22 @@ ASM_TOOL_NAMES <- ASM_TOOL_NAMES[c(
     snakemake@config$assemblers$hy
 )]
 # colors
-ASM_TOOL_PALETTE1 <- ggsci::pal_nejm("default", alpha=1)(5)
-ASM_TOOL_PALETTE2 <- ggsci::pal_nejm("default", alpha=0.8)(5)
-ASM_TOOL_PALETTE3 <- ggsci::pal_nejm("default", alpha=0.6)(5)
-ASM_TOOL_PALETTE4 <- ggsci::pal_nejm("default", alpha=0.4)(5)
+ASM_TOOL_PALETTE1 <- ggsci::pal_nejm("default", alpha=1)(7)
+ASM_TOOL_PALETTE2 <- ggsci::pal_nejm("default", alpha=0.8)(7)
+ASM_TOOL_PALETTE3 <- ggsci::pal_nejm("default", alpha=0.6)(7)
+ASM_TOOL_PALETTE4 <- ggsci::pal_nejm("default", alpha=0.4)(7)
 ASM_TOOL_COLORS <- c(
     # LR, SR, hybrid
     "Flye"=ASM_TOOL_PALETTE1[1],
-    "MEGAHIT"=ASM_TOOL_PALETTE1[2],
-    "metaSPAdes"=ASM_TOOL_PALETTE1[3],
-    "OPERA-MS"=ASM_TOOL_PALETTE1[4],
-    "metaSPAdes (H)"=ASM_TOOL_PALETTE1[5],
-    # polishing w/ metaT (w/o LR)
-    "Racon(MEGAHIT + metaT)"=ASM_TOOL_PALETTE2[2],
-    "Racon(metaSPAdes + metaT)"=ASM_TOOL_PALETTE2[3],
-    "Racon(OPERA-MS + metaT)"=ASM_TOOL_PALETTE2[4],
-    "Racon(metaSPAdes (H) + metaT)"=ASM_TOOL_PALETTE2[5]
+    "wtdbg2"=ASM_TOOL_PALETTE1[2],
+    "MEGAHIT"=ASM_TOOL_PALETTE1[3],
+    "metaSPAdes"=ASM_TOOL_PALETTE1[4],
+    "OPERA-MS"=ASM_TOOL_PALETTE1[5],
+    "metaSPAdes (H)"=ASM_TOOL_PALETTE1[6],
+    "IMP3 (MG/MT)"=ASM_TOOL_PALETTE1[7]
 )
 ASM_TOOL_COLORS <- ASM_TOOL_COLORS[ASM_TOOL_NAMES]
 
-###############
-# Gene tools
-# GENE_TOOL_NAMES <- c(
-#     "prodigal_partial"="Prodigal (partial)",
-#     "prodigal_total"="Prodigal (total)",
-#     "cdhit_unique"="CD-HIT (unique)",
-#     "cdhit_total"="CD-HIT (total)"
-# )
-
 ###############
 # CRISPR tools