绘制marker基因表达热图的时候总是报错

这是我的命令

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

我检查过了celltype的分组名字没有问题,基因名称也可以在.qs找到,但是它一直报错

这是报错

 [ reached 'max' / getOption("max.print") -- omitted 1 rows ]

As of Seurat v5, we recommend using AggregateExpression to perform pseudo-bulk analysis.

This message is displayed once per session.

Removing cells with NA for 1 or more grouping variables

Names of identity class contain underscores ('_'), replacing with dashes ('-')

This message is displayed once every 8 hours.

First group.by variable `ident` starts with a number, appending `g` to ensure valid variable names

This message is displayed once every 8 hours.

Error in htdf[, cluster.order] : subscript out of bounds

Calls: averageHeatmap

In addition: Warning message:

Removing 12158 cells missing data for vars requested 

Execution halted

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1 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

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
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