Comments (3)
When I changed "st_labels" to "st_label" in line 110 of R_utils.R, another error message appeared in the same line.
run real data...
[1] "Generating synthetic test spots..."
|======================================================================| 100%
[1] "Generation of 1000 test spots took 0.21 mins"
[1] "output consists of a list with two dataframes, this first one has the weighted count matrix and the second has the metadata for each spot"
Error in[.data.frame
(do.call("rbind", rep(list(st_label[[1]]), round(N2/N1) + :
undefined columns selected
Calls: Convert_Data -> data_process -> [ -> [.data.frame
Execution halted
My guess is that line 110 in R_utils.R may be changed from 1 to 2?
(Changed st_labels[[1]] to st_label[[1]] and [1:N2] to [1:N2,])
- label.list2 <- do.call("rbind", rep(list(st_labels[[1]]), round(N2/N1)+1))[1:N2]
- label.list2 <- do.call("rbind", rep(list(st_label[[1]]), round(N2/N1)+1))[1:N2,]
Thanks!
from dstg.
When I changed the line 110 in R_utils.R as above, I crossed with another error.
[1] "Generation of 1000 test spots took 0.2 mins"
[1] "output consists of a list with two dataframes, this first one has the weighted count matrix and the second has the metadata for each spot"
Error in label.list[[i]] : subscript out of bounds
Calls: Convert_Data ... eval.parent -> eval -> eval -> write.table -> is.data.frame
Execution halted
Is it possibly related to "label.list[[i]]" in line 149 in R_utils.R? I presumed that since "label.list" contains the single-cell annotation data and its length is 1, label.list[[i]] needs to be changed to st.label[[i]] defined in line 126 (From 1 to 2 below).
- write.csv(label.list[[i]],file=paste0(inforDir,'/ST_label/ST_label_',i,'.csv'),quote=F)
- write.csv(st.label[[i]],file=paste0(inforDir,'/ST_label/ST_label_',i,'.csv'),quote=F)
It seems that all the issues are resolved by changing line 110 and 149 as above.
Could you check on with the issues?
Thank you!
from dstg.
When I changed "st_labels" to "st_label" in line 110 of R_utils.R, another error message appeared in the same line.
run real data...
[1] "Generating synthetic test spots..."
|======================================================================| 100%
[1] "Generation of 1000 test spots took 0.21 mins"
[1] "output consists of a list with two dataframes, this first one has the weighted count matrix and the second has the metadata for each spot"
Error in[.data.frame
(do.call("rbind", rep(list(st_label[[1]]), round(N2/N1) + :
undefined columns selected
Calls: Convert_Data -> data_process -> [ -> [.data.frame
Execution haltedMy guess is that line 110 in R_utils.R may be changed from 1 to 2?
(Changed st_labels[[1]] to st_label[[1]] and [1:N2] to [1:N2,])
- label.list2 <- do.call("rbind", rep(list(st_labels[[1]]), round(N2/N1)+1))[1:N2]
- label.list2 <- do.call("rbind", rep(list(st_label[[1]]), round(N2/N1)+1))[1:N2,]
Thanks!
It should be correct if changing "st_labels" to "st_label" in line 110 of R_utils.R. I will verify and modify it. However, I am not sure about the other errors that you mentioned. I will check on my side or can you share me your toy data that I can check?
from dstg.
Related Issues (20)
- Predict_output.csv problem HOT 4
- what filterEdge filters? HOT 3
- error while running demo HOT 1
- Number of genes in the ST dataset HOT 3
- Problem with Matrix Subsetting in convert_data.R HOT 1
- 'test_spot_fun' is no longer supported HOT 1
- The demo fails to run HOT 1
- Question regarding the link-graph usage in the main training script HOT 2
- Question regarding the data files. HOT 1
- Issue in data_process function in R_utils.R HOT 1
- problem in running train.py
- Error on synthetic dataset HOT 2
- Datasets in paper
- Data format of our own data HOT 11
- Is there an implementation of pytorch version? HOT 2
- PDAC data HOT 4
- code bug HOT 3
- PBMC data HOT 1
- Clarification on the input matrices HOT 15
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from dstg.