Comments (15)
from cellrouter.
Dear Edroaldo,
Thanks. Here is the dimension, they are different, does this cause the error? How should I fix it? Thanks.
dim([email protected])
[1] 29408 4859
dim([email protected])
[1] 4391 34
from cellrouter.
from cellrouter.
Dear Edroaldo,
Thanks. I tried and it still showed the same error...
Here is the code:
data <- as.data.frame(as.matrix([email protected][,rownames([email protected])]))
cellrouter <- CellRouter(rawdata=as.data.frame(data), min.cells=0, min.genes=0)
[1] "Initializing CellRouter object"
dim(data)
[1] 29408 4391
dim([email protected])
[1] 4391 34
cellrouter <- addInfo(cellrouter, metadata = [email protected], colname = 'merged_20_Aug', metadata.column='res.0.8')
Error in rep(colors, times = replicate_row) : invalid 'times' argument
Best,
Kun
from cellrouter.
from cellrouter.
Dear Edroaldo,
I tried to make the variable and called the addInfo, but met with the same error...
My Seurat object has many different annotation, need I delete some?
Best,
Kun
from cellrouter.
from cellrouter.
Dear Edroaldo,
Sorry for the delayed reply, just had a meeting.
Here is the info:
from cellrouter.
from cellrouter.
Dear Edroaldo,
Sorry, it's my fault. All these column names contain "D", I deleted it to keep them in one line. But left some... All other info are correct. So, I guess it's not because of this. Sorry about this.
Can you check if there are any other issue? Thanks.
Best,Kun
from cellrouter.
from cellrouter.
from cellrouter.
Dear Edroaldo,
Sorry about the delayed reply, have so many things to handle today.
Here is the info:
cellrouter@rawdata[1:5,1:5]
D2T_AAAGTAGAGAACAATC D2T_ACGAGCCCAATCGGTT D2T_AGGGAGTAGTGACATA D2T_CACACAACACTCGACG D2T_CAGTAACTCGCGCCAA
RP11-34P13.7 0 0 0 0 0
AL627309.1 0 0 0 0 0
AP006222.2 0 0 0 0 1
RP4-669L17.10 0 0 0 1 0
RP11-206L10.3 0 0 0 0 0
cellrouter@ndata[1:5,1:5]
D2T_AAAGTAGAGAACAATC D2T_ACGAGCCCAATCGGTT D2T_AGGGAGTAGTGACATA D2T_CACACAACACTCGACG D2T_CAGTAACTCGCGCCAA
RP11-34P13.7 0 0 0 0 0
AL627309.1 0 0 0 0 0
AP006222.2 0 0 0 0 1
RP4-669L17.10 0 0 0 1 0
RP11-206L10.3 0 0 0 0 0
class([email protected])
[1] "data.frame"
Best,
Kun
from cellrouter.
from cellrouter.
Thank you Edroaldo for all efforts, I'll re-make the object, and see if it works.
Thanks,
Kun
from cellrouter.
Related Issues (20)
- Creating a clean featureplot
- suitable Normalization for cellrouter - scran vs scone vs SCnorm HOT 5
- Gene filtering method & count formats HOT 5
- PlotTrajectory without smoothening? Genes that should be relatively constant are not? HOT 1
- plotPathHeatmap function "invalid 'row.names' length" HOT 5
- Overlay TSNE with Cellrouter trajectory HOT 4
- Seurat to cellrouter error HOT 3
- mean.p and mean.np stand for? HOT 2
- findPaths: argument 1 is not a vector HOT 1
- Error in processTrajectories HOT 8
- Heatmaps with multiple metadata annotations HOT 2
- processTrajectories HOT 2
- I am getting all error when coming back to cellrouter after a year HOT 2
- findPaths can't find cellrouter main class
- "could not find function"
- in Linux -- Could not find or load main class cellrouter.CellRouter HOT 1
- could not find function "graph.data.frame" when running buildGRN on example code HOT 3
- Java error in "findPaths"
- processtrajectories error HOT 1
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from cellrouter.