search

BaderLab / Tempora

Pathway-based trajectory inference method for time-series scRNAseq data
MIT License
25 stars 6 forks source link

Error in IdentifyVaryingPWs() #5

Closed Pestudkaru closed 4 years ago

Pestudkaru commented 4 years ago

Hi! I get the same error with both the tutorial mouse data set and also with my own data. Error in IdentifyVaryingPWs(cortex_tempora, pval_threshold = 0.05) : object 'plot_df' not found

Also in the CalculatePWProfiles() function the part with parallelization "parallel.sz = DetectCores()-2)" has changed for some reason to detectCores(). Maybe between update 3.6.2 and 3.6.3 they changed the capitalization.

thinh-tran commented 4 years ago

Hi! This was an issue with some special characters in the pathways' names that I didn't account for. I updated the function to take care of these special cases and that should fix it - can you try again?

Thanks for pointing out the case change in detectCores() - I'll update the vignette.

Pestudkaru commented 4 years ago

Hi! So now I get an error already at the first step: ImportSeuratObject() Extracting data... Extracting metadata... Creating Tempora object...Error in CreateTemporaObject(data, meta.data = metadata, timepoint_order = timepoint_order, : object 'celltype_markers' not found And again it happens both with my data and with the mouse cortex data.

thinh-tran commented 4 years ago

ImportSeuratObject() now takes a celltype_markers parameter to perform automated cluster labeling in case the clusters are not already labeled - I documented this in the manual page of the function but haven't yet written it up on the main GitHub page, sorry about the confusion! In your case, you can pass celltype_markers = NULL to ImportSeuratObject() and that'll take care of it.

zhangjiaobxy commented 4 years ago

Hello, I got the same error in IdentifyVaryingPWs() as below: 

> cortex_tempora <- IdentifyVaryingPWs(cortex_tempora, pval_threshold = 0.05)
Fitting GAM models...Error in IdentifyVaryingPWs(cortex_tempora, pval_threshold = 0.05) : 
  object 'plot_df' not found

I am using the tutorial MouseCortex.RData data. I am using Mouse_GOBP_AllPathways_no_GO_iea_April_01_2020_symbol.gmt in function CalculatePWProfiles(), because I can not find the Mouse_GOBP_AllPathways_no_GO_iea_September_01_2019_symbol.gmt file on the website (http://download.baderlab.org/EM_Genesets/current_release/).

Any help will be appreciated, thanks a lot!