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llrs
llrs
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I get error code: rror in plotOrderedColors(dendro$order, colors = colors, rowLabels = rowLabels, : ERROR: length of colors vector not compatible with number of objects in 'order'.

Using the followingerror code:


net= blockwiseModules(Th1_h5, power=6,
                      TOMType = "signed", minModuleSize=30,
                      reassignThreshold =0, mergeCutHeight = 0.25,
                      numericLabels = TRUE, pamRespectsDendro = FALSE,
                      saveTOMs = TRUE,
                      saveTOMFileBase = "PBCreponseTOMB",
                      verbose= 3 
mergedColorsError =in labels2colors(net$colors)

plotDendroAndColorsplotOrderedColors(net$dendrograms[[1]], mergedColors[net$blockGenes[[1]]],
                    "Module colors",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUEdendro$order, guideHang = 0.05)
moduleLabels = net$colors
moduleColors = labels2colors(net$colors)
MEs = net$MEs
geneTree = net$dendrograms[[1]]

bwet = blockwiseModules(Th1_h5, maxBlockSize = 8000,
                        power=6, TOMType = "signed", minModuleSize = 30,
                        reassignThreshold = 0, mergeCutHeight = 0.25,
                        numericLabels = TRUE,
                        saveTOMs = TRUE, 
                        saveTOMFileBase = "Th1_NR_R_TOM-blockwise",
                        verbose=3)
bwLabels = matchLabels(bwet$colors,moduleLabels)

bwModuleColors = labels2colors(bwLabels)


plotDendroAndColors(geneTree,
                    cbind(moduleColors, bwModuleColors),
                    c("Single block", "2 blocks"),
                    main = "Single block gene dendrogram and module colours"colors,
                    dendroLabelsrowLabels = FALSErowLabels, hang =: 0.03,
              ERROR: length of colors vector not addGuidecompatible =with TRUE,number guideHangof =objects in 0'order'.05)

Using the following code:

net= blockwiseModules(Th1_h5, power=6,
                      TOMType = "signed", minModuleSize=30,
                      reassignThreshold =0, mergeCutHeight = 0.25,
                      numericLabels = TRUE, pamRespectsDendro = FALSE,
                      saveTOMs = TRUE,
                      saveTOMFileBase = "PBCreponseTOMB",
                      verbose= 3 
mergedColors = labels2colors(net$colors)

plotDendroAndColors(net$dendrograms[[1]], mergedColors[net$blockGenes[[1]]],
                    "Module colors",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang = 0.05)
moduleLabels = net$colors
moduleColors = labels2colors(net$colors)
MEs = net$MEs
geneTree = net$dendrograms[[1]]

bwet = blockwiseModules(Th1_h5, maxBlockSize = 8000,
                        power=6, TOMType = "signed", minModuleSize = 30,
                        reassignThreshold = 0, mergeCutHeight = 0.25,
                        numericLabels = TRUE,
                        saveTOMs = TRUE, 
                        saveTOMFileBase = "Th1_NR_R_TOM-blockwise",
                        verbose=3)
bwLabels = matchLabels(bwet$colors,moduleLabels)

bwModuleColors = labels2colors(bwLabels)


plotDendroAndColors(geneTree,
                    cbind(moduleColors, bwModuleColors),
                    c("Single block", "2 blocks"),
                    main = "Single block gene dendrogram and module colours",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang =  0.05)

I get error code: rror in plotOrderedColors(dendro$order, colors = colors, rowLabels = rowLabels, : ERROR: length of colors vector not compatible with number of objects in 'order'.

Using the following code:


net= blockwiseModules(Th1_h5, power=6,
                      TOMType = "signed", minModuleSize=30,
                      reassignThreshold =0, mergeCutHeight = 0.25,
                      numericLabels = TRUE, pamRespectsDendro = FALSE,
                      saveTOMs = TRUE,
                      saveTOMFileBase = "PBCreponseTOMB",
                      verbose= 3 
mergedColors = labels2colors(net$colors)

plotDendroAndColors(net$dendrograms[[1]], mergedColors[net$blockGenes[[1]]],
                    "Module colors",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang = 0.05)
moduleLabels = net$colors
moduleColors = labels2colors(net$colors)
MEs = net$MEs
geneTree = net$dendrograms[[1]]

bwet = blockwiseModules(Th1_h5, maxBlockSize = 8000,
                        power=6, TOMType = "signed", minModuleSize = 30,
                        reassignThreshold = 0, mergeCutHeight = 0.25,
                        numericLabels = TRUE,
                        saveTOMs = TRUE, 
                        saveTOMFileBase = "Th1_NR_R_TOM-blockwise",
                        verbose=3)
bwLabels = matchLabels(bwet$colors,moduleLabels)

bwModuleColors = labels2colors(bwLabels)


plotDendroAndColors(geneTree,
                    cbind(moduleColors, bwModuleColors),
                    c("Single block", "2 blocks"),
                    main = "Single block gene dendrogram and module colours",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang =  0.05)

I get the error code:

Error in plotOrderedColors(dendro$order, colors = colors, rowLabels = rowLabels,  : 
  ERROR: length of colors vector not compatible with number of objects in 'order'.

Using the following code:

net= blockwiseModules(Th1_h5, power=6,
                      TOMType = "signed", minModuleSize=30,
                      reassignThreshold =0, mergeCutHeight = 0.25,
                      numericLabels = TRUE, pamRespectsDendro = FALSE,
                      saveTOMs = TRUE,
                      saveTOMFileBase = "PBCreponseTOMB",
                      verbose= 3 
mergedColors = labels2colors(net$colors)

plotDendroAndColors(net$dendrograms[[1]], mergedColors[net$blockGenes[[1]]],
                    "Module colors",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang = 0.05)
moduleLabels = net$colors
moduleColors = labels2colors(net$colors)
MEs = net$MEs
geneTree = net$dendrograms[[1]]

bwet = blockwiseModules(Th1_h5, maxBlockSize = 8000,
                        power=6, TOMType = "signed", minModuleSize = 30,
                        reassignThreshold = 0, mergeCutHeight = 0.25,
                        numericLabels = TRUE,
                        saveTOMs = TRUE, 
                        saveTOMFileBase = "Th1_NR_R_TOM-blockwise",
                        verbose=3)
bwLabels = matchLabels(bwet$colors,moduleLabels)

bwModuleColors = labels2colors(bwLabels)


plotDendroAndColors(geneTree,
                    cbind(moduleColors, bwModuleColors),
                    c("Single block", "2 blocks"),
                    main = "Single block gene dendrogram and module colours",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang =  0.05)
added 1266 characters in body
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holly
holly
  • 47
  • 6

net= blockwiseModules(Th1_h5, power=6,
                      TOMType = "signed", minModuleSize=30,
                      reassignThreshold =0, mergeCutHeight = 0.25,
                      numericLabels = TRUE, pamRespectsDendro = FALSE,
                      saveTOMs = TRUE,
                      saveTOMFileBase = "PBCreponseTOMB",
                      verbose= 3 
mergedColors = labels2colors(net$colors)

plotDendroAndColors(net$dendrograms[[1]], mergedColors[net$blockGenes[[1]]],
                    "Module colors",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang = 0.05)
moduleLabels = net$colors
moduleColors = labels2colors(net$colors)
MEs = net$MEs
geneTree = net$dendrograms[[1]]

bwet = blockwiseModules(Th1_h5, maxBlockSize = 8000,
                        power=6, TOMType = "signed", minModuleSize = 30,
                        reassignThreshold = 0, mergeCutHeight = 0.25,
                        numericLabels = TRUE,
                        saveTOMs = TRUE, 
                        saveTOMFileBase = "Th1_NR_R_TOM-blockwise",
                        verbose=3)
bwLabels = matchLabels(bwet$colors,moduleLabels)

bwModuleColors = labels2colors(bwLabels)


plotDendroAndColors(geneTree,
                    cbind(moduleColors, bwModuleColors),
                    c("Single block", "2 blocks"),
                    main = "Single block gene dendrogram and module colours",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang =  0.05)  







plotDendroAndColors(geneTree,
                    cbind(moduleColors, bwModuleColors),
                    c("Single block", "2 blocks"),
                    main = "Single block gene dendrogram and module colours",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang =  0.05) 





net= blockwiseModules(Th1_h5, power=6,
                      TOMType = "signed", minModuleSize=30,
                      reassignThreshold =0, mergeCutHeight = 0.25,
                      numericLabels = TRUE, pamRespectsDendro = FALSE,
                      saveTOMs = TRUE,
                      saveTOMFileBase = "PBCreponseTOMB",
                      verbose= 3 
mergedColors = labels2colors(net$colors)

plotDendroAndColors(net$dendrograms[[1]], mergedColors[net$blockGenes[[1]]],
                    "Module colors",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang = 0.05)
moduleLabels = net$colors
moduleColors = labels2colors(net$colors)
MEs = net$MEs
geneTree = net$dendrograms[[1]]

bwet = blockwiseModules(Th1_h5, maxBlockSize = 8000,
                        power=6, TOMType = "signed", minModuleSize = 30,
                        reassignThreshold = 0, mergeCutHeight = 0.25,
                        numericLabels = TRUE,
                        saveTOMs = TRUE, 
                        saveTOMFileBase = "Th1_NR_R_TOM-blockwise",
                        verbose=3)
bwLabels = matchLabels(bwet$colors,moduleLabels)

bwModuleColors = labels2colors(bwLabels)


plotDendroAndColors(geneTree,
                    cbind(moduleColors, bwModuleColors),
                    c("Single block", "2 blocks"),
                    main = "Single block gene dendrogram and module colours",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang =  0.05)  
Source Link
holly
holly
  • 47
  • 6

Error Code in WGCNA: Dealing with large data sets: block-wise network construction andmodule detection

I am comparing single block module detection with 2 block module detection in WGCNA.

Does anyone know what this relates to? I have rechecked and rechecked my codes for both the single and 2 module detection and cannot see an error. Thank you

I get error code: rror in plotOrderedColors(dendro$order, colors = colors, rowLabels = rowLabels, : ERROR: length of colors vector not compatible with number of objects in 'order'.

Using the following code:

plotDendroAndColors(geneTree,
                    cbind(moduleColors, bwModuleColors),
                    c("Single block", "2 blocks"),
                    main = "Single block gene dendrogram and module colours",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang =  0.05)