Did any one face this error?
augur<- calculate_auc(zebra,label_col="Timepoint", cell_type_col = "seurat_clusters")
using default assay: RNA ...
| | 0%, ETA NAError in mutate():
ℹ In argument: metrics = pred %>% map(metric_fun).
Caused by error in map():
ℹ In index: 1.
ℹ With name: 1.
Caused by error in metric_set():
! Failed to compute accuracy().
Caused by error:
✖ truth and estimate levels must be equivalent.
• truth: Control, 3 dpi, 7 dpi, 21 dpi, and 42 dpi.
• estimate: 21 dpi, 3 dpi, 42 dpi, 7 dpi, and Control.
Run rlang::last_trace() to see where the error occurred.
Warning messages:
1: In apply_fun(unique(cell_types), mc.cores = n_threads, function(cell_type) { :
mc.cores > 1 is not supported on Windows due to limitation of mc*apply() functions.
mc.core is set to 1.
2: There were 6 warnings in mutate().
The first warning was:
ℹ In argument: pred = pmap(pred, retrieve_class_preds).
Caused by warning in levels(test$label) == colnames(tbl):
! longer object length is not a multiple of shorter object length
ℹ Run dplyr::last_dplyr_warnings() to see the 5 remaining warnings.
My code is as follow:
library(dplyr)
library(Seurat)
library(ggplot2)
library(Augur)
zebra<- readRDS(file = "ekab_NeuronalSubset_complete_labelled_010725.rds")
augur<- calculate_auc(zebra,label_col="Timepoint", cell_type_col = "seurat_clusters")
The levels of the timepoint are defined like following
levels(zebra$Timepoint)
[1] "Control" "3 dpi" "7 dpi" "21 dpi" "42 dpi"
I am not sure how to set both truth and estimate levels the same??
Did any one face this error?
augur<- calculate_auc(zebra,label_col="Timepoint", cell_type_col = "seurat_clusters")
using default assay: RNA ...
| | 0%, ETA NAError in
mutate():ℹ In argument:
metrics = pred %>% map(metric_fun).Caused by error in
map():ℹ In index: 1.
ℹ With name: 1.
Caused by error in
metric_set():! Failed to compute
accuracy().Caused by error:
✖
truthandestimatelevels must be equivalent.•
truth: Control, 3 dpi, 7 dpi, 21 dpi, and 42 dpi.•
estimate: 21 dpi, 3 dpi, 42 dpi, 7 dpi, and Control.Run
rlang::last_trace()to see where the error occurred.Warning messages:
1: In apply_fun(unique(cell_types), mc.cores = n_threads, function(cell_type) { :
mc.cores > 1 is not supported on Windows due to limitation of mc*apply() functions.
mc.core is set to 1.
2: There were 6 warnings in
mutate().The first warning was:
ℹ In argument:
pred = pmap(pred, retrieve_class_preds).Caused by warning in
levels(test$label) == colnames(tbl):! longer object length is not a multiple of shorter object length
ℹ Run dplyr::last_dplyr_warnings() to see the 5 remaining warnings.
My code is as follow:
library(dplyr)
library(Seurat)
library(ggplot2)
library(Augur)
zebra<- readRDS(file = "ekab_NeuronalSubset_complete_labelled_010725.rds")
augur<- calculate_auc(zebra,label_col="Timepoint", cell_type_col = "seurat_clusters")
The levels of the timepoint are defined like following
levels(zebra$Timepoint)
[1] "Control" "3 dpi" "7 dpi" "21 dpi" "42 dpi"
I am not sure how to set both truth and estimate levels the same??