error reporting for rankSimilarity

[zh-zhang1984]

Hi, thank you for your excellent package; but I CANNOT successfully solve the following issues:

cellchat <- computeNetSimilarityPairwise(cellchat, type = "functional")
cellchat <- netEmbedding(cellchat, type = "functional",
                         umap.method = "uwot")
cellchat <- netClustering(
  cellchat, type = "functional")
netVisual_embeddingPairwise(
  cellchat, type = "functional", label.size = 3.5)
rankSimilarity(cellchat, type = "functional")
Compute the distance of signaling networks between datasets 1 2 
Error in data1[i, ] : subscript out of bounds

The previous lines works well , but the last line of rankSimilarity reported error, do you have any hints for this?

[sqjin]

@zh-zhang1984 I am sorry I have no idea on this error. I can take a look if you can share me your object. You can also run the source codes line by line to figure out the reason.

[zh-zhang1984]

Then I decompose the function and found the rowname of Y is NULL:

> Y <- methods::slot(cellchat, slot.name)$similarity[[type]]$dr[[comparison.name]]
> Y
            [,1]        [,2]
 [1,] -2.4558424  3.90435387
 [2,] -2.2896808  0.96898676
 [3,] -2.7028822  4.67414261
 [4,] -1.7700657  0.87971998
 [5,] -2.4533371  4.19529177
 [6,] -2.3673338  3.28581263
 [7,] -1.3741516  0.95044757
 [8,] -2.6882185  2.34379078
 [9,] -2.3985704  2.57968689
[10,] -2.2128395 -4.13564967

> rownames(Y)
NULL

Is there any hints for this bug?

[sqjin]

@zh-zhang1984 I have no idea on this error. I can take a look if you can share me your object or provide a small example to replicate your error.

[zh-zhang1984]

Zhongheng Zhang has shared a OneDrive file with you. To view it, click the link below. https://1drv.ms/u/s!AnooFyHsUDdzghVsIZ-IzFCsSXJg [https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]https://1drv.ms/u/s!AnooFyHsUDdzghVsIZ-IzFCsSXJg cellchat.rdshttps://1drv.ms/u/s!AnooFyHsUDdzghVsIZ-IzFCsSXJg

enclosed is the cellchat object that report this error; thank you, Zhongheng

---

From: Suoqin Jin @.> Sent: Saturday, October 9, 2021 2:09 AM To: sqjin/CellChat @.> Cc: Zhongheng Zhang @.>; Mention @.> Subject: Re: [sqjin/CellChat] error reporting for rankSimilarity (#259)

@zh-zhang1984https://github.com/zh-zhang1984 I have no idea on this error. I can take a look if you can share me your object or provide a small example to replicate your error.

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[HopeStar2018]

Hi, thank you for your excellent package; but I CANNOT successfully solve the following issues:

cellchat <- computeNetSimilarityPairwise(cellchat, type = "functional")
cellchat <- netEmbedding(cellchat, type = "functional",
                         umap.method = "uwot")
cellchat <- netClustering(
  cellchat, type = "functional")
netVisual_embeddingPairwise(
  cellchat, type = "functional", label.size = 3.5)
rankSimilarity(cellchat, type = "functional")
Compute the distance of signaling networks between datasets 1 2 
Error in data1[i, ] : subscript out of bounds

The previous lines works well , but the last line of rankSimilarity reported error, do you have any hints for this?

张老师，我也发生了相同的问题，我发现 rankSimilarity()中，有一个提取rowname的函数： Y <- methods::slot(object, slot.name)$similarity[[type]]$dr[[comparison.name]] 这个提取出来的Y的rowname为 NULL，这个是不对的，所以我在后面自己加了一条代码，给Y的rowname进行了赋值，应该就可以跑通了； rownames(Y) <- rownames(cellchat@netP[["similarity"]]$functional$matrix$1-2) group <- sub(".*--", "", rownames(Y)) 麻烦问一下，这个问题您是怎么解决呢？谢谢 ～

[yudalang3]

我相信我找到出错的原因了。我看了 netEmbedding/netClustering/netVisual_embedding的源代码，我发现netVisual_embedding这里，少了一个if else。

I believe I have found the reason for the mistake. I watched netEmbedding/netClustering/netVisual_embedding source code, I found netVisual_embedding here, less an if the else.

[aboutfanfan]

我相信我找到出错的原因了。我看了 netEmbedding/netClustering/netVisual_embedding的源代码，我发现netVisual_embedding这里，少了一个if else。

我相信我已经找到了错误的原因。我看了netEmbedding/netClustering/netVisual_embedding源代码，我在这里找到了netVisual_embedding，而不是其他。

Can you share the changed function file? Thank you!

[sqjin]

@aboutfanfan I think the current codes in CellChat is correct.