update zstat metric

littlecabiria · littlecabiria · commit a741028b7b5d · 2025-03-06T22:03:12.000+11:00
diff --git a/src/metrics/ks_statistic_gene_cell/config.vsh.yaml b/src/metrics/ks_statistic_gene_cell/config.vsh.yaml
@@ -8,7 +8,7 @@ links:
 
 info:
   metrics:
-    - name: ks_statistic_frac_zero_genes
+    - name: ks_statistic_frac_zero_genes_zstat
       label: Fraction of zeros per gene
       summary: KS statistic of the fraction of zeros per gene.
       description: |
@@ -18,7 +18,7 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
-    - name: ks_statistic_frac_zero_cells
+    - name: ks_statistic_frac_zero_cells_zstat
       label: Fraction of zeros per cell
       summary: KS statistic of the fraction of zeros per spot (cell).
       description: |
@@ -28,7 +28,7 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
-    - name: ks_statistic_lib_size_cells
+    - name: ks_statistic_lib_size_cells_zstat
       label: Library size
       summary: KS statistic of the library size.
       description: |
@@ -38,7 +38,7 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
-    - name: ks_statistic_efflib_size_cells
+    - name: ks_statistic_efflib_size_cells_zstat
       label: Effective library size
       summary: KS statistic of the effective library size.
       description: |
@@ -48,7 +48,7 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
-    - name: ks_statistic_tmm_cells
+    - name: ks_statistic_tmm_cells_zstat
       label: TMM
       summary: KS statistic of the weight trimmed mean of M-values normalization factor (TMM).
       description: |
@@ -58,7 +58,7 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
-    - name: ks_statistic_scaled_var_cells
+    - name: ks_statistic_scaled_var_cells_zstat
       label: Scaled variance cell
       summary: KS statistic of the spot- (or cell-) level scaled variance of the expression matrix.
       description: |
@@ -68,7 +68,7 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
-    - name: ks_statistic_scaled_mean_cells
+    - name: ks_statistic_scaled_mean_cells_zstat
       label: Scaled mean cells
       summary: KS statistic of the spot- (or cell-) level scaled mean of the expression matrix.
       description: |
@@ -78,7 +78,7 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
-    - name: ks_statistic_lib_fraczero_cells
+    - name: ks_statistic_lib_fraczero_cells_zstat
       label: Library size vs fraction zero
       summary: KS statistic of the relationship between library size and the proportion of zeros per spot (cell).
       description: |
@@ -88,7 +88,7 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
-    - name: ks_statistic_pearson_cells
+    - name: ks_statistic_pearson_cells_zstat
       label: Sample Pearson correlation
       summary: KS statistic of the sample Pearson correlation.
       description: |
@@ -98,7 +98,7 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
-    - name: ks_statistic_scaled_var_genes
+    - name: ks_statistic_scaled_var_genes_zstat
       label: Scaled variance genes
       summary: KS statistic of the gene-level scaled variance of the expression matrix.
       description: |
@@ -108,7 +108,7 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
-    - name: ks_statistic_scaled_mean_genes
+    - name: ks_statistic_scaled_mean_genes_zstat
       label: Scaled mean genes
       summary: KS statistic of the gene-level scaled mean of the expression matrix.
       description: |
@@ -118,7 +118,7 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
-    - name: ks_statistic_pearson_genes
+    - name: ks_statistic_pearson_genes_zstat
       label: Gene Pearson correlation
       summary: KS statistic of the gene Pearson correlation.
       description: |
@@ -128,7 +128,7 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
-    - name: ks_statistic_mean_var_genes
+    - name: ks_statistic_mean_var_genes_zstat
       label: Mean vs variance
       summary: KS statistic of the relationship between mean expression and variance expression.
       description: |
@@ -138,7 +138,7 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
-    - name: ks_statistic_mean_fraczero_genes
+    - name: ks_statistic_mean_fraczero_genes_zstat
       label: Mean vs fraction zero
       summary: KS statistic of the relationship between mean expression and the proportion of zero per gene.
       description: |
@@ -148,6 +148,147 @@ info:
       maximize: false
       references:
         doi: 10.1201/9780429485572
+    - name: ks_statistic_frac_zero_genes_tstat
+      label: Fraction of zeros per gene
+      summary: KS statistic of the fraction of zeros per gene.
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the fraction of zeros per gene in the real datasets versus the fraction of zeros per gene in the simulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+    - name: ks_statistic_frac_zero_cells_tstat
+      label: Fraction of zeros per cell
+      summary: KS statistic of the fraction of zeros per spot (cell).
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the fraction of zeros per spot (cell) in the real datasets versus the fraction of zeros per spot (cell) in the simulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+    - name: ks_statistic_lib_size_cells_tstat
+      label: Library size
+      summary: KS statistic of the library size.
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the total sum of UMI counts across all genes in the real datasets versus the total sum of UMI counts across all genes in the simmulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+    - name: ks_statistic_efflib_size_cells_tstat
+      label: Effective library size
+      summary: KS statistic of the effective library size.
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the effective library size of the real datasets versus the effective library size of the simulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+    - name: ks_statistic_tmm_cells_tstat
+      label: TMM
+      summary: KS statistic of the weight trimmed mean of M-values normalization factor (TMM).
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the weight trimmed mean of M-values normalization factor for the real datasets versus the weight trimmed mean of M-values normalization factor for the simulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+    - name: ks_statistic_scaled_var_cells_tstat
+      label: Scaled variance cell
+      summary: KS statistic of the spot- (or cell-) level scaled variance of the expression matrix.
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the spot-level z-score standardization of the variance of expression matrix in terms of log2(CPM) in the real datasets versus the simulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+    - name: ks_statistic_scaled_mean_cells_tstat
+      label: Scaled mean cells
+      summary: KS statistic of the spot- (or cell-) level scaled mean of the expression matrix.
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the z-score standardization of the mean of expression matrix in terms of log2(CPM) in the real datasets versus the simulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+    - name: ks_statistic_lib_fraczero_cells_tstat
+      label: Library size vs fraction zero
+      summary: KS statistic of the relationship between library size and the proportion of zeros per spot (cell).
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the relationship between library size and the proportion of zeros per spot (cell) in the real datasets versus the simulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+    - name: ks_statistic_pearson_cells_tstat
+      label: Sample Pearson correlation
+      summary: KS statistic of the sample Pearson correlation.
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the sample Pearson correlation of the real datasets versus the sample Pearson correlation of the simulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+    - name: ks_statistic_scaled_var_genes_tstat
+      label: Scaled variance genes
+      summary: KS statistic of the gene-level scaled variance of the expression matrix.
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the gene-level z-score standardization of the variance of expression matrix in terms of log2(CPM) in the real datasets versus the simulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+    - name: ks_statistic_scaled_mean_genes_tstat
+      label: Scaled mean genes
+      summary: KS statistic of the gene-level scaled mean of the expression matrix.
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the gene-level z-score standardization of the mean of expression matrix in terms of log2(CPM) in the real datasets versus the simulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+    - name: ks_statistic_pearson_genes_tstat
+      label: Gene Pearson correlation
+      summary: KS statistic of the gene Pearson correlation.
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the gene Pearson correlation of the real datasets versus the gene Pearson correlation of the simulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+    - name: ks_statistic_mean_var_genes_tstat
+      label: Mean vs variance
+      summary: KS statistic of the relationship between mean expression and variance expression.
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the relationship between mean expression and variance expression in the real datasets versus the simulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+    - name: ks_statistic_mean_fraczero_genes_tstat
+      label: Mean vs fraction zero
+      summary: KS statistic of the relationship between mean expression and the proportion of zero per gene.
+      description: |
+        The Kolmogorov-Smirnov statistic comparing the relationship between mean expression and the proportion of zero per gene in the real datasets versus the simulated datasets.
+      min: -Inf
+      max: +Inf
+      maximize: false
+      references:
+        doi: 10.1201/9780429485572
+
 
 resources:
   - type: r_script
diff --git a/src/metrics/ks_statistic_gene_cell/script.R b/src/metrics/ks_statistic_gene_cell/script.R
@@ -105,20 +105,36 @@ ks_statistic_mean_fraczero_genes <- ks::kde.test(x1 = mean_fraczero_real_genes,
 
 cat("Combining metric values\n")
 uns_metric_ids <- c(
-  "ks_statistic_frac_zero_genes",
-  "ks_statistic_frac_zero_cells",
-  "ks_statistic_lib_size_cells",
-  "ks_statistic_efflib_size_cells",
-  "ks_statistic_tmm_cells",
-  "ks_statistic_scaled_var_cells",
-  "ks_statistic_scaled_mean_cells",
-  "ks_statistic_lib_fraczero_cells",
-  "ks_statistic_pearson_cells",
-  "ks_statistic_scaled_var_genes",
-  "ks_statistic_scaled_mean_genes",
-  "ks_statistic_pearson_genes",
-  "ks_statistic_mean_var_genes",
-  "ks_statistic_mean_fraczero_genes"
+  "ks_statistic_frac_zero_genes_zstat",
+  "ks_statistic_frac_zero_cells_zstat",
+  "ks_statistic_lib_size_cells_zstat",
+  "ks_statistic_efflib_size_cells_zstat",
+  "ks_statistic_tmm_cells_zstat",
+  "ks_statistic_scaled_var_cells_zstat",
+  "ks_statistic_scaled_mean_cells_zstat",
+  "ks_statistic_lib_fraczero_cells_zstat",
+  "ks_statistic_pearson_cells_zstat",
+  "ks_statistic_scaled_var_genes_zstat",
+  "ks_statistic_scaled_mean_genes_zstat",
+  "ks_statistic_pearson_genes_zstat",
+  "ks_statistic_mean_var_genes_zstat",
+  "ks_statistic_mean_fraczero_genes_zstat",
+
+  "ks_statistic_frac_zero_genes_tstat",
+  "ks_statistic_frac_zero_cells_tstat",
+  "ks_statistic_lib_size_cells_tstat",
+  "ks_statistic_efflib_size_cells_tstat",
+  "ks_statistic_tmm_cells_tstat",
+  "ks_statistic_scaled_var_cells_tstat",
+  "ks_statistic_scaled_mean_cells_tstat",
+  "ks_statistic_lib_fraczero_cells_tstat",
+  "ks_statistic_pearson_cells_tstat",
+  "ks_statistic_scaled_var_genes_tstat",
+  "ks_statistic_scaled_mean_genes_tstat",
+  "ks_statistic_pearson_genes_tstat",
+  "ks_statistic_mean_var_genes_tstat",
+  "ks_statistic_mean_fraczero_genes_tstat"
+
 )
 uns_metric_values <- c(
   ks_statistic_frac_zero_genes$zstat,
@@ -134,7 +150,22 @@ uns_metric_values <- c(
   ks_statistic_scaled_mean_genes$zstat,
   ks_statistic_pearson_genes$zstat,
   ks_statistic_mean_var_genes$zstat,
-  ks_statistic_mean_fraczero_genes$zstat
+  ks_statistic_mean_fraczero_genes$zstat,
+  
+  ks_statistic_frac_zero_genes$tstat,
+  ks_statistic_frac_zero_cells$tstat,
+  ks_statistic_lib_size_cells$tstat,
+  ks_statistic_efflib_size_cells$tstat,
+  ks_statistic_tmm_cells$tstat,
+  ks_statistic_scaled_var_cells$tstat,
+  ks_statistic_scaled_mean_cells$tstat,
+  ks_statistic_lib_fraczero_cells$tstat,
+  ks_statistic_pearson_cells$tstat,
+  ks_statistic_scaled_var_genes$tstat,
+  ks_statistic_scaled_mean_genes$tstat,
+  ks_statistic_pearson_genes$tstat,
+  ks_statistic_mean_var_genes$tstat,
+  ks_statistic_mean_fraczero_genes$tstat
 )
 
 cat("Writing output AnnData to file\n")
