Error in SpaCET.visualize.colocalization(SpaCET_obj)

[Smilenone]

When I use SpaCET.visualize.colocalization(SpaCET_obj), I met an error:

Error in levels<-(*tmp*, value = as.character(levels)) :
factor level [41] is duplicated

Can you help?

[beibeiru]

Hi,

Can you upload your SpaCET_obj to the following link? I will fix it soon. Thanks.

Best,
Beibei

[Smilenone]

Sure, I have done that. Best, Qunlun.

…

------------------ 原始邮件 ------------------ 发件人: "data2intelligence/SpaCET" ***@***.***>; 发送时间: 2023年3月20日(星期一) 晚上9:12 ***@***.***>; 抄送: "Qunlun ***@***.******@***.***>; 主题: Re: [data2intelligence/SpaCET] Error in SpaCET.visualize.colocalization(SpaCET_obj) (Issue #10) Hi, Can you upload your SpaCET_obj to the following link? I will fix it soon. Thanks. https://connecthkuhk-my.sharepoint.com/:f:/g/personal/bbru_connect_hku_hk/ElaCd5LWwH5KtsFNTtCSLssB1UuqijfDxcFuJDxiQzxkXg?e=okiHal Best, Beibei — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[beibeiru]

Hi, Qunlun,

The error is caused by the duplicated sublineages (i.e., Macro TNFRSF9) of Myeloid in your customized lineageTree.

SpaCET_obj@results$deconvolution$Ref$lineageTree$Myeloid
 [1] "Macro TNFRSF9"   "Macro SPP1"      "DC2 CD1A"        "DC1"             "DC2 PLAC8"       "Myeloid cycling"
 [7] "Mono FCN1"       "Macro CCL5"      "Macro MSR1"      "Macro TNFRSF9"

There are two options to fix it. You can choose either one.

1. Reinstall the latest version of SpaCET. Then, run SpaCET.visualize.colocalization(SpaCET_obj).
2. You don't need to reinstall. Just revise your SpaCET_obj by the following code.

SpaCET_obj@results$deconvolution$Ref$lineageTree$Myeloid <- 
unique(SpaCET_obj@results$deconvolution$Ref$lineageTree$Myeloid)

Thanks.

Best,
Beibei

[Smilenone]

Hi Beibei, I would like to thank you for your timely response, which solved my problem perfectly. Best, Qunlun

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------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "data2intelligence/SpaCET" ***@***.***&gt;; 发送时间:&nbsp;2023年3月22日(星期三) 凌晨5:20 ***@***.***&gt;; 抄送:&nbsp;"Qunlun ***@***.******@***.***&gt;; 主题:&nbsp;Re: [data2intelligence/SpaCET] Error in SpaCET.visualize.colocalization(SpaCET_obj) (Issue #10) Hi, Qunlun, The error is caused by the duplicated sublineages (i.e., Macro TNFRSF9) of Myeloid in your customized lineageTree. ***@***.***$deconvolution$Ref$lineageTree$Myeloid [1] "**Macro TNFRSF9**" "Macro SPP1" "DC2 CD1A" "DC1" "DC2 PLAC8" "Myeloid cycling" [7] "Mono FCN1" "Macro CCL5" "Macro MSR1" "**Macro TNFRSF9**" There are two options to fix it. You can choose either one. Reinstall the latest version of SpaCET. Then, run SpaCET.visualize.colocalization(SpaCET_obj). You don't need to reinstall. Just revise your SpaCET_obj by the following code. ***@***.***$deconvolution$Ref$lineageTree$Myeloid <- ***@***.***$deconvolution$Ref$lineageTree$Myeloid) Thanks. Best, Beibei — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***&gt;