report: updated names/colors of assemblers in utils.R

workflow_report/scripts/utils.R

@@ -398,10 +398,15 @@ ASM_TOOL_NAMES <- c(
     "flye"="Flye",
     "wtdbg2"="wtdbg2",
     "canu"="Canu",
+    "flye_sr"="Flye + racon(SR)",
+    "wtdbg2_sr"="wtdbg2 + racon(SR)",
+    "canu_sr"="Canu + racon(SR)",
     "megahit"="MEGAHIT",
     "metaspades"="metaSPAdes",
     "operams"="OPERA-MS",
     "metaspadeshybrid"="metaSPAdes (H)",
+    "operams_sr"="OPERA-MS + racon(SR)",
+    "metaspadeshybrid_sr"="metaSPAdes (H) + racon(SR)",
     "imp3"="IMP3 (MG/MT)"
 )
 # select assemblers from config
@@ -417,13 +422,18 @@ ASM_TOOL_PALETTE2 <- ggsci::pal_nejm("default", alpha=0.8)(8)
 ASM_TOOL_PALETTE3 <- ggsci::pal_nejm("default", alpha=0.6)(8)
 ASM_TOOL_PALETTE4 <- ggsci::pal_nejm("default", alpha=0.4)(8)
 ASM_TOOL_COLORS <- c(
-    "Flye"=ASM_TOOL_PALETTE1[1],
-    "wtdbg2"=ASM_TOOL_PALETTE1[2],
-    "Canu"=ASM_TOOL_PALETTE1[3],
+    "Flye"=ASM_TOOL_PALETTE2[1],
+    "wtdbg2"=ASM_TOOL_PALETTE2[2],
+    "Canu"=ASM_TOOL_PALETTE2[3],
+    "Flye + racon(SR)"=ASM_TOOL_PALETTE1[1],
+    "wtdbg2 + racon(SR)"=ASM_TOOL_PALETTE1[2],
+    "Canu + racon(SR)"=ASM_TOOL_PALETTE1[3],
     "MEGAHIT"=ASM_TOOL_PALETTE1[4],
     "metaSPAdes"=ASM_TOOL_PALETTE1[5],
-    "OPERA-MS"=ASM_TOOL_PALETTE1[6],
-    "metaSPAdes (H)"=ASM_TOOL_PALETTE1[7],
+    "OPERA-MS"=ASM_TOOL_PALETTE2[6],
+    "metaSPAdes (H)"=ASM_TOOL_PALETTE2[7],
+    "OPERA-MS + racon(SR)"=ASM_TOOL_PALETTE1[6],
+    "metaSPAdes (H) + racon(SR)"=ASM_TOOL_PALETTE1[7],
     "IMP3 (MG/MT)"=ASM_TOOL_PALETTE1[8]
 )
 ASM_TOOL_COLORS <- ASM_TOOL_COLORS[ASM_TOOL_NAMES]