HVG genes setting through files

scanpy-scripts-tests.bats

@@ -28,7 +28,11 @@ setup() {
     norm_opt="--save-layer filtered -t 10000 -l all -n after -X ${norm_mtx} --show-obj stdout"
     norm_obj="${output_dir}/norm.h5ad"
     hvg_opt="-m 0.0125 3 -d 0.5 inf -s --show-obj stdout"
+    always_hvg="${data_dir}/always_hvg.txt"
+    never_hvg="${data_dir}/never_hvg.txt"
+    hvg_opt_always_never="--always-hv-genes-file ${always_hvg} --never-hv-genes-file ${never_hvg}"
     hvg_obj="${output_dir}/hvg.h5ad"
+    hvg_obj_on_off="${output_dir}/hvg_on_off.h5ad"
     regress_opt="-k n_counts --show-obj stdout"
     regress_obj="${output_dir}/regress.h5ad"
     scale_opt="--save-layer normalised -m 10 --show-obj stdout"
@@ -131,6 +135,22 @@ setup() {
     [ -f "$raw_matrix_from_raw" ]
 }
 
+@test "Add genes to be considered HVGs" {
+    if [ "$resume" = 'true' ] && [ -f "$always_hvg" ]; then
+        skip "$always_hvg exists"
+    fi
+
+    run eval "echo -e 'MIR1302-10\nFAM138A' > $always_hvg"
+}
+
+@test "Add genes not to be considered HVGs" {
+    if [ "$resume" = 'true' ] && [ -f "$never_hvg" ]; then
+        skip "$never_hvg exists"
+    fi
+
+    run eval "echo -e 'ISG15\nTNFRSF4' > $never_hvg"
+}
+
 @test "Test MTX write from layers" {
     if [ "$resume" = 'true' ] && [ -f "$raw_matrix_from_layer" ]; then
         skip "$raw_matrix exists"
@@ -219,6 +239,14 @@ setup() {
     [ -f  "$hvg_obj" ]
 }
 
+@test "Find variable genes with optional turn on/off lists" {
+    if [ "$resume" = 'true' ] && [ -f "$hvg_obj_on_off" ]; then
+        skip "$hvg_obj_on_off exists and resume is set to 'true'"
+    fi
+
+    run rm -f $hvg_obj_on_off && eval "$scanpy hvg $hvg_opt_always_never $norm_obj $hvg_obj_on_off"
+}
+
 # Do separate doublet simulation step (normally we'd just let the main scrublet
 # process do this).
 

scanpy_scripts/cmd_options.py

@@ -3,13 +3,14 @@
 """
 
 import click
+
 from .click_utils import (
     CommaSeparatedText,
     Dictionary,
-    valid_limit,
-    valid_parameter_limits,
     mutually_exclusive_with,
     required_by,
+    valid_limit,
+    valid_parameter_limits,
 )
 
 COMMON_OPTIONS = {
@@ -856,6 +857,20 @@
             "'seurat_v3', ties are broken by the median (across batches) rank based on "
             "within-batch normalized variance.",
         ),
+        click.option(
+            "--always-hv-genes-file",
+            "always_hv_genes_file",
+            type=click.Path(exists=True),
+            default=None,
+            help="If specified, the gene identifers in this file will be set as highly variable in the var dataframe after HVGs are computed.",
+        ),
+        click.option(
+            "--never-hv-genes-file",
+            "never_hv_genes_file",
+            type=click.Path(exists=True),
+            default=None,
+            help="If specified, the gene identifers in this file will be removed from highly variable in the var dataframe (set to false) after HVGs are computed.",
+        ),
     ],
     "scale": [
         *COMMON_OPTIONS["input"],

scanpy_scripts/lib/_hvg.py

@@ -21,6 +21,20 @@ def hvg(
     if "n_top_genes" in kwargs and kwargs["n_top_genes"] is not None:
         kwargs["n_top_genes"] = min(adata.n_vars, kwargs["n_top_genes"])
 
+    always_hv_genes = None
+    if "always_hv_genes_file" in kwargs and kwargs["always_hv_genes_file"] is not None:
+        with open(kwargs["always_hv_genes_file"], "r") as f:
+            always_hv_genes = f.read().splitlines()
+
+    never_hv_genes = None
+    if "never_hv_genes_file" in kwargs and kwargs["never_hv_genes_file"] is not None:
+        with open(kwargs["never_hv_genes_file"], "r") as f:
+            never_hv_genes = f.read().splitlines()
+
+    # to avoid upsetting the scanpy function with unexpected keyword arguments
+    del kwargs["always_hv_genes_file"]
+    del kwargs["never_hv_genes_file"]
+
     sc.pp.highly_variable_genes(
         adata,
         min_mean=mean_limits[0],
@@ -30,4 +44,35 @@ def hvg(
         **kwargs,
     )
 
+    return switch_hvgs(adata, always_hv_genes, never_hv_genes)
+
+
+def switch_hvgs(adata, always_hv_genes=None, never_hv_genes=None):
+    """
+    Function to switch on/off highly variable genes based on a list of genes.
+
+    >>> adata = sc.datasets.pbmc3k()
+    >>> sc.pp.normalize_total(adata)
+    >>> sc.pp.log1p(adata)
+    >>> sc.pp.highly_variable_genes(adata)
+    >>> adata = switch_hvgs(adata, always_hv_genes=['MIR1302-10', 'FAM138A'], never_hv_genes=['ISG15', 'TNFRSF4'])
+    >>> adata.var.loc['ISG15'].highly_variable
+    False
+    >>> adata.var.loc['TNFRSF4'].highly_variable
+    False
+    >>> adata.var.loc['MIR1302-10'].highly_variable
+    True
+    >>> adata.var.loc['CPSF3L'].highly_variable
+    True
+    """
+    if always_hv_genes is not None:
+        adata.var.highly_variable = np.logical_or(
+            adata.var.highly_variable, adata.var_names.isin(always_hv_genes)
+        )
+
+    if never_hv_genes is not None:
+        adata.var.highly_variable = np.logical_and(
+            adata.var.highly_variable, ~adata.var_names.isin(never_hv_genes)
+        )
+
     return adata