你的细胞类型名字里面有特殊字符 / 需要把每个细胞名字用双引号引起来试试的;
Rscript $scripts/averageHeatmap.r \
-i benihoppe_flower.added.celltype.qs \
--group.by celltype \
--group.order "g0-Early-organ-primordium" \
"g1-Sepal-protoderm" "g2-Perianth-primordium" \
"g3-Inflorescence-stem-primordium" \
"g4-Sepal" "g5-Cell-cycle-S-phase" \
"g6-cambium" "g7-Stressed-perianth" "g8-Pedicel" \
"g9-Cortex" "g10-Cell-cycle-G2/M-phase" "g11-Anther" \
"g12-Meristem" "g13-Cell-cycle-M-phase" "g14-Capal" \
"g15-Tapetum" "g16-Cell-cycle-G1/S-phase" "g17-Petal" \
"g18-Defense-front-line-cells" "g19-Floral-Protoderm" \
--markerGene "FxaBH_7A_001279" "FxaBH-1D-001232" \
"FxaBH-1B-002238" \
"FxaBH-6B-003083" "FxaBH-3B-003733" "FxaBH-7C-000376" \
"FxaBH-4C-001213" "FxaBH-7B-003095" "FxaBH-6A-001569" \
"FxaBH-6C-002604" "FxaBH-5A-003386" \
"FxaBH-2D-003106" "FxaBH-6C-001696" "FxaBH-2C-003244" \
"FxaBH-5C-002444" "FxaBH-5A-002887" \
"FxaBH-3C-000417" "FxaBH-6C-000564" \
"FxaBH-3A-004603" "FxaBH-1D-001733" \
"FxaBH-4A-003251" "FxaBH-3C-003261" \
"FxaBH-7C-001287" "FxaBH-3D-000845" "FxaBH-7A-001211" \
"FxaBH-2B-002567" "FxaBH-6D-002844" "FxaBH-5C-002444" \
"FxaBH-7A-001416" "FxaBH-2B-000056" "FxaBH-2A-001576" \
"FxaBH-2B-003539" "FxaBH-3C-003726" "FxaBH-5B-002206" \
"FxaBH-5A-000651" "FxaBH-6D-000946" "FxaBH-4B-001948" \
"FxaBH-4D-001878" "FxaBH-6B-001741" \
"FxaBH-6C-003399" "FxaBH-5B-002892" "FxaBH-7B-000191" \
"FxaBH-7B-003068" "FxaBH-3D-000157" \
"FxaBH-5B-003435" "FxaBH-7C-002093" \
"FxaBH-2B-003397" "FxaBH-6D-000285" \
"FxaBH-5A-001614" "FxaBH-6A-005030" \
"FxaBH-6D-000531" "FxaBH-6A-001752" \
"FxaBH-2B-001927" "FxaBH-2A-003245" \
"FxaBH-4A-002180" "FxaBH-7C-001276" \
"FxaBH-1A-000401" "FxaBH-6A-000602" \
"FxaBH-7C-002501" "FxaBH-4A-000818" \
"FxaBH-6A-000954" "FxaBH-6D-002953" "FxaBH-6B-002282" \
"FxaBH-6A-002712" "FxaBH-5D-003212" \
-p all_Marker.celltype.heatmap -H 40 -W 50
