diff --git a/nb/scrna.html b/nb/scrna.html index 453cf4d..b19c838 100644 --- a/nb/scrna.html +++ b/nb/scrna.html @@ -15313,7 +15313,7 @@
Matplotlib is building the font cache; this may take a moment. --
adata.obs['batch'] #sample label - the data contains 15 separate samples
@@ -15794,7 +15774,7 @@ Data analysis
-In [11]:
+In [14]:
adata.var.head()
@@ -15858,7 +15838,7 @@ Data analysis
-In [12]:
+In [15]:
adata.var['n_cells_by_counts'] #nr of cells showing transcripts of a gene
@@ -15979,7 +15959,7 @@ Data analysis
-In [13]:
+In [16]:
MT = ['MT-' in i for i in adata.var_names] #a vector with True and False to find MT genes
@@ -16065,7 +16045,7 @@ Quality Filtering
-In [14]:
+In [17]:
sc.pl.scatter(adata, x='total_counts', y='n_genes_by_counts', color='perc_mito',
@@ -16118,7 +16098,7 @@ Quality Filtering
-In [15]:
+In [18]:
sc.pl.scatter(adata[adata.obs['n_genes_by_counts']<3000], x='total_counts', y='n_genes_by_counts', color='perc_mito',
@@ -16171,7 +16151,7 @@ Quality Filtering
-In [16]:
+In [19]:
fig = px.histogram(adata[adata.obs['total_counts']<20000].obs, x='total_counts', nbins=100,
@@ -16228,9 +16208,9 @@ Quality Filtering
-