Skip to content

Commit

Permalink
update README
Browse files Browse the repository at this point in the history
  • Loading branch information
@stemangiola
stemangiola committed Dec 21, 2022
1 parent 66f11e7 commit cf1fac3
Show file tree
Hide file tree
Showing 7 changed files with 35 additions and 31 deletions.
64 changes: 34 additions & 30 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -81,16 +81,16 @@ counts_obj |>
## # A tibble: 72 × 18
## cell_group parameter factor c_lower c_eff…¹ c_upper c_pH0 c_FDR c_n_eff
## <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 B1 (Intercept) <NA> 0.869 1.06 1.24 0 0 4529.
## 2 B1 typecancer type -1.21 -0.878 -0.538 0 0 4296.
## 3 B2 (Intercept) <NA> 0.423 0.697 0.959 5.00e-4 3.75e-5 3358.
## 4 B2 typecancer type -1.21 -0.784 -0.363 3.75e-3 6.11e-4 4084.
## 5 B3 (Intercept) <NA> -0.643 -0.383 -0.136 7.17e-2 4.01e-3 5204.
## 6 B3 typecancer type -0.616 -0.224 0.137 4.54e-1 1.37e-1 4037.
## 7 BM (Intercept) <NA> -1.27 -1.02 -0.754 0 0 5698.
## 8 BM typecancer type -0.764 -0.347 0.0320 2.24e-1 3.62e-2 4352.
## 9 CD4 1 (Intercept) <NA> 0.121 0.324 0.522 1.03e-1 1.15e-2 3652.
## 10 CD4 1 typecancer type -0.110 0.157 0.425 6.36e-1 2.19e-1 2916.
## 1 B1 (Intercept) <NA> 0.873 1.06 1.23 0 0 4746.
## 2 B1 typecancer type -1.23 -0.878 -0.527 2.50e-4 6.25e-5 2626.
## 3 B2 (Intercept) <NA> 0.415 0.691 0.950 7.50e-4 6.25e-5 5154.
## 4 B2 typecancer type -1.21 -0.772 -0.351 5.50e-3 8.33e-4 4362.
## 5 B3 (Intercept) <NA> -0.632 -0.387 -0.152 6.07e-2 3.38e-3 4135.
## 6 B3 typecancer type -0.605 -0.225 0.142 4.47e-1 1.39e-1 3179.
## 7 BM (Intercept) <NA> -1.29 -1.02 -0.750 0 0 4836.
## 8 BM typecancer type -0.756 -0.346 0.0353 2.35e-1 5.7 e-2 3588.
## 9 CD4 1 (Intercept) <NA> 0.116 0.322 0.509 1.12e-1 1.15e-2 3516.
## 10 CD4 1 typecancer type -0.103 0.164 0.435 6.04e-1 2.20e-1 2549.
## # … with 62 more rows, 9 more variables: c_R_k_hat <dbl>, v_lower <dbl>,
## # v_effect <dbl>, v_upper <dbl>, v_pH0 <dbl>, v_FDR <dbl>, v_n_eff <dbl>,
## # v_R_k_hat <dbl>, count_data <list>, and abbreviated variable name ¹​c_effect
Expand All @@ -116,16 +116,16 @@ seurat_obj |>
## # A tibble: 60 × 18
## cell_group param…¹ factor c_lower c_eff…² c_upper c_pH0 c_FDR c_n_eff
## <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 B immature typeca… type -2.01 -1.57 -1.12 0 0 NA
## 2 B immature typehe… type 1.12 1.57 2.01 0 0 NA
## 3 B mem typeca… type -2.31 -1.71 -1.11 0 0 NA
## 4 B mem typehe… type 1.11 1.71 2.31 0 0 NA
## 5 CD4 cm high c… typeca… type 0.940 1.86 3.00 0 0 NA
## 6 CD4 cm high c… typehe… type -3.00 -1.86 -0.940 0 0 NA
## 7 CD4 cm riboso… typeca… type 0.571 1.24 1.97 1.50e-3 3.89e-4 NA
## 8 CD4 cm riboso… typehe… type -1.97 -1.24 -0.571 1.50e-3 3.89e-4 NA
## 9 CD4 cm S100A4 typeca… type -1.24 -0.882 -0.540 2.50e-4 5.00e-5 NA
## 10 CD4 cm S100A4 typehe… type 0.540 0.882 1.24 2.50e-4 5.00e-5 NA
## 1 B immature typeca… type -2.03 -1.58 -1.12 0 0 NA
## 2 B immature typehe… type 1.12 1.58 2.03 0 0 NA
## 3 B mem typeca… type -2.51 -1.93 -1.34 0 0 NA
## 4 B mem typehe… type 1.34 1.93 2.51 0 0 NA
## 5 CD4 cm high c… typeca… type 0.952 1.86 2.93 2.50e-4 5.00e-5 NA
## 6 CD4 cm high c… typehe… type -2.93 -1.86 -0.952 2.50e-4 5.00e-5 NA
## 7 CD4 cm riboso… typeca… type 0.553 1.25 2.00 1.00e-3 2.81e-4 NA
## 8 CD4 cm riboso… typehe… type -2.00 -1.25 -0.553 1.00e-3 2.81e-4 NA
## 9 CD4 cm S100A4 typeca… type -1.27 -0.886 -0.540 0 0 NA
## 10 CD4 cm S100A4 typehe… type 0.540 0.886 1.27 0 0 NA
## # … with 50 more rows, 9 more variables: c_R_k_hat <dbl>, v_lower <dbl>,
## # v_effect <dbl>, v_upper <dbl>, v_pH0 <dbl>, v_FDR <dbl>, v_n_eff <dbl>,
## # v_R_k_hat <dbl>, count_data <list>, and abbreviated variable names
Expand Down Expand Up @@ -182,6 +182,10 @@ loo_compare(
)
```

## elpd_diff se_diff
## model1 0.0 0.0
## model2 -79.9 11.3

## Differential variability, binary factor

We can model the cell-group variability also dependent on the type, and
Expand All @@ -205,16 +209,16 @@ res
## # A tibble: 60 × 18
## cell_group param…¹ factor c_lower c_eff…² c_upper c_pH0 c_FDR c_n_eff
## <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 B immature (Inter… <NA> 0.582 0.965 1.33 5.00e-4 5.36e-5 5635.
## 2 B immature typehe… type 0.967 1.49 2.00 0 0 3507.
## 3 B mem (Inter… <NA> -1.65 -1.08 -0.467 3.00e-3 4.03e-4 3873.
## 4 B mem typehe… type 1.24 2.00 2.75 2.50e-4 8.33e-5 3301.
## 5 CD4 cm high c… (Inter… <NA> -0.831 -0.390 0.103 2.08e-1 3.12e-2 4146.
## 6 CD4 cm high c… typehe… type -3.19 -1.39 1.51 1.86e-1 4.81e-2 2131.
## 7 CD4 cm riboso… (Inter… <NA> 0.166 0.491 0.850 4.10e-2 2.82e-3 3992.
## 8 CD4 cm riboso… typehe… type -2.45 -1.74 -0.841 2.25e-3 6.25e-4 4160.
## 9 CD4 cm S100A4 (Inter… <NA> 1.76 2.01 2.26 0 0 6267.
## 10 CD4 cm S100A4 typehe… type 0.337 0.743 1.16 2.50e-3 1.00e-3 3289.
## 1 B immature (Inter… <NA> 0.599 0.967 1.33 2.50e-4 1.92e-5 5475.
## 2 B immature typehe… type 0.972 1.48 2.01 0 0 3797.
## 3 B mem (Inter… <NA> -1.65 -1.08 -0.485 3.00e-3 2.50e-4 3272.
## 4 B mem typehe… type 1.29 1.99 2.76 0 0 2681.
## 5 CD4 cm high c… (Inter… <NA> -0.829 -0.389 0.107 2.07e-1 2.40e-2 4299.
## 6 CD4 cm high c… typehe… type -3.24 -1.39 1.47 1.98e-1 4.96e-2 2844.
## 7 CD4 cm riboso… (Inter… <NA> 0.158 0.499 0.857 4.00e-2 2.76e-3 3827.
## 8 CD4 cm riboso… typehe… type -2.47 -1.75 -0.825 1.75e-3 6.00e-4 2875.
## 9 CD4 cm S100A4 (Inter… <NA> 1.76 2.01 2.26 0 0 6613.
## 10 CD4 cm S100A4 typehe… type 0.364 0.739 1.15 2.50e-3 9.17e-4 4323.
## # … with 50 more rows, 9 more variables: c_R_k_hat <dbl>, v_lower <dbl>,
## # v_effect <dbl>, v_upper <dbl>, v_pH0 <dbl>, v_FDR <dbl>, v_n_eff <dbl>,
## # v_R_k_hat <dbl>, count_data <list>, and abbreviated variable names
Expand Down
Binary file modified inst/figures/unnamed-chunk-12-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified inst/figures/unnamed-chunk-13-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified inst/figures/unnamed-chunk-14-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified inst/figures/unnamed-chunk-15-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified inst/figures/unnamed-chunk-16-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
2 changes: 1 addition & 1 deletion man/fragments/intro.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,7 @@ This is achieved through model comparison with `loo`. In the following example,
If `elpd_diff` is away from zero of \> 5 `se_diff` difference of 5, we are confident that a model is better than the other [reference](https://discourse.mc-stan.org/t/interpreting-elpd-diff-loo-package/1628/2?u=stemangiola).
In this case, -79.9 / 11.5 = -6.9, therefore we can conclude that model one, the one with factor association, is better than model two.

```{r, eval=FALSE, message=FALSE, warning=FALSE}
```{r, message=FALSE, warning=FALSE}
library(loo)
# Fit first model
Expand Down

0 comments on commit cf1fac3

Please sign in to comment.