Removal of "projectData" function in CellChat

[AydinHerik]

Hi, projectData is not included in the current version of the CellChat package:

ls("package:CellChat") [1] "addMeta"
[2] "addReduction"
[3] "aggregateNet"
[4] "barPlot"
[5] "barplot_internal"
[6] "buildSNN"
[7] "CellChat_theme_opts"
[8] "CellChatDB.human"
[9] "CellChatDB.mouse"
[10] "CellChatDB.zebrafish"
[11] "checkGeneSymbol"
[12] "colorRamp3"
[13] "compareInteractions"
[14] "computeAveExpr"
[15] "computeCellDistance"
[16] "computeCommunProb"
[17] "computeCommunProbPathway"
[18] "computeEigengap"
[19] "computeEnrichmentScore"
[20] "computeExpr_agonist"
[21] "computeExpr_antagonist"
[22] "computeExpr_complex"
[23] "computeExpr_coreceptor"
[24] "computeExpr_LR"
[25] "computeExprGroup_agonist"
[26] "computeExprGroup_antagonist"
[27] "computeLaplacian"
[28] "computeNetD_structure"
[29] "computeNetSimilarity"
[30] "computeNetSimilarityPairwise"
[31] "computeRegionDistance"
[32] "createCellChat"
[33] "dotPlot"
[34] "extractEnrichedLR"
[35] "extractGene"
[36] "extractGeneSubset"
[37] "extractGeneSubsetFromPair"
[38] "filterCommunication"
[39] "findEnrichedSignaling"
[40] "geometricMean"
[41] "getMaxWeight"
[42] "ggPalette"
[43] "identifyCommunicationPatterns"
[44] "identifyEnrichedInteractions"
[45] "identifyOverExpressedGenes"
[46] "identifyOverExpressedInteractions"
[47] "identifyOverExpressedLigandReceptor"
[48] "liftCellChat"
[49] "mergeCellChat"
[50] "mergeInteractions"
[51] "netAnalysis_computeCentrality"
[52] "netAnalysis_contribution"
[53] "netAnalysis_diff_signalingRole_scatter" [54] "netAnalysis_dot"
[55] "netAnalysis_river"
[56] "netAnalysis_signalingChanges_scatter"
[57] "netAnalysis_signalingRole_heatmap"
[58] "netAnalysis_signalingRole_network"
[59] "netAnalysis_signalingRole_scatter"
[60] "netClustering"
[61] "netEmbedding"
[62] "netMappingDEG"
[63] "netVisual"
[64] "netVisual_aggregate"
[65] "netVisual_barplot"
[66] "netVisual_bubble"
[67] "netVisual_chord_cell"
[68] "netVisual_chord_cell_internal"
[69] "netVisual_chord_gene"
[70] "netVisual_circle"
[71] "netVisual_diffInteraction"
[72] "netVisual_embedding"
[73] "netVisual_embeddingPairwise"
[74] "netVisual_embeddingPairwiseZoomIn"
[75] "netVisual_embeddingZoomIn"
[76] "netVisual_heatmap"
[77] "netVisual_hierarchy1"
[78] "netVisual_hierarchy2"
[79] "netVisual_individual"
[80] "netVisual_spatial"
[81] "normalizeData"
[82] "pieChart"
[83] "plotGeneExpression"
[84] "PPI.human"
[85] "PPI.mouse"
[86] "rankNet"
[87] "rankNetPairwise"
[88] "rankSimilarity"
[89] "runCellChatApp"
[90] "runPCA"
[91] "runUMAP"
[92] "scaleData"
[93] "scaleMat"
[94] "scPalette"
[95] "searchPair"
[96] "selectK"
[97] "setIdent"
[98] "showDatabaseCategory"
[99] "sketchData"
[100] "smoothData"
[101] "spatialDimPlot"
[102] "spatialFeaturePlot"
[103] "StackedVlnPlot"
[104] "subsetCellChat"
[105] "subsetCommunication"
[106] "subsetData"
[107] "subsetDB"
[108] "triMean"
[109] "updateCCC_score"
[110] "updateCellChat"
[111] "updateCellChatDB"
[112] "updateClusterLabels"

[cleiti]

Hi, i'm not from cellchat team but it seems to have been renamed to smoothData according to #169 . The only problem is that it's still named projectData in tutorials.

[yuanG2000]

hi, I use smoothData function,but encounter this error cellchat <- smoothData(cellchat, PPI.human) Error in smoothData(cellchat, PPI.human) : is(adj, "matrix") || is(adj, "sparseMatrix") is not TRUE

[cleiti]

Hi, i've had the same problem as well. The syntax is cellchat <- smoothData(cellchat, adj = PPI.human) , specifying the adj parameter. Once again, better documentation is needed.

[yuanG2000]

Hi, i've had the same problem as well. The syntax is cellchat <- smoothData(cellchat, adj = PPI.human) , specifying the adj parameter. Once again, better documentation is needed.

thanks a lot,I solve the problem

[AydinHerik]

Thank you all for the clarification @Cleiti @yuanG2000 ! This helped solve my issue.

[HBYCZWY]

thank you all of the above answers！！！

[amulya-saini]

Hi, i've had the same problem as well. The syntax is cellchat <- smoothData(cellchat, adj = PPI.human) , specifying the adj parameter. Once again, better documentation is needed.

Thank you!!

[hemiao8912]

adj = PPI.human

Thanks a lot

[Harmony714]

Thanks a lot！！New documentation is needed！

[AlbertoFabbri93]

Can anyone from the team update the documentation please?

[AnonymousGym]

cellchat <- smoothData(cellchat, PPI.human) Error in smoothData(cellchat, PPI.human) : is(adj, "matrix") || is(adj, "sparseMatrix") is not TRUE

this problem is still not solved.

[XLulu0519]

cellchat <- smoothData(cellchat, PPI.human) Error in smoothData(cellchat, PPI.human) : is(adj, "matrix") || is(adj, "sparseMatrix") is not TRUE

this problem is still not solved.

You need to specify the adj parameter. cellchat <- smoothData(cellchat, adj = PPI.human)

[peterCCChen]

cellchat <- smoothData(cellchat, PPI.human) Error in smoothData(cellchat, PPI.human) : is(adj, "matrix") || is(adj, "sparseMatrix") is not TRUE this problem is still not solved.

You need to specify the adj parameter. cellchat <- smoothData(cellchat, adj = PPI.human) I just updated to the latest version of CellChat V2 today ,；I found the same problem with PPI. My solution is as follows：data(PPI.human) library(Matrix) PPI.human <- as(PPI.human, "sparseMatrix") cellchat <- smoothData(cellchat, adj = PPI.human)

[Hanis-gatech]

It looks like projectData is working now and smoothData isn't. Can anyone confirm that? I tried using adj with smoothData. It says that smoothData is not a function in CellChat

[Hanis-gatech]

confirming that the following works! smoothData doesn't work anymore cellchat <- projectData(cellchat, PPI.human)

[ciiri]

Thanks a lot！！