Remove unintuitive st_preprocess_fig_size param

Remove the unintuitive `st_preprocess_fig_size` parameter. This was only
used one occasion in the pipeline, where it only affected a single
report figure - all other figures hard hard-coded sizes. This brings all
figures in line in that all sizes are hard-coded.

This should possibly be changed in the future, but giving users the
ability to change figure sizes on a pipeline-level would be difficult,
since it may be that not all figures can look good with the same size
across the board.

bin/st_qc_and_normalisation.qmd

@@ -24,7 +24,6 @@ resolution = 1
 saveFileST = None
 
 rawAdata = None  # Name of the h5ad file
-pltFigSize = 6  # Figure size
 minCounts = 500  # Min counts per spot
 minGenes = 250  # Min genes per spot
 minCells = 1  # Min cells per gene
@@ -44,7 +43,7 @@ import matplotlib.pyplot as plt
 import seaborn as sns
 from IPython.display import display, Markdown
 
-plt.rcParams["figure.figsize"] = (pltFigSize, pltFigSize)
+plt.rcParams["figure.figsize"] = (6, 6)
 ```
 
 ## Anndata object
@@ -113,15 +112,15 @@ p = sns.histplot(
   st_adata.obs["total_counts"], kde=True, ax=axs[0, 0]
 ).set(title=f"Total counts")
 p = sns.histplot(
-  st_adata.obs["total_counts"][st_adata.obs["total_counts"] < histplotQCmaxTotalCounts], 
+  st_adata.obs["total_counts"][st_adata.obs["total_counts"] < histplotQCmaxTotalCounts],
   kde=True,
   bins=histplotQCbins,
   ax=axs[0, 1]
 ).set(title=f"Total counts < {histplotQCmaxTotalCounts}")
 p = sns.histplot(
-  st_adata.obs["n_genes_by_counts"], 
-  kde=True, 
-  bins=histplotQCbins, 
+  st_adata.obs["n_genes_by_counts"],
+  kde=True,
+  bins=histplotQCbins,
   ax=axs[1, 0]
 ).set(title=f"Genes by counts")
 p = sns.histplot(
@@ -186,15 +185,15 @@ p = sns.histplot(
   st_adata.obs["total_counts"], kde=True, ax=axs[0, 0]
 ).set(title=f"Total counts")
 p = sns.histplot(
-  st_adata.obs["total_counts"][st_adata.obs["total_counts"] < histplotQCmaxTotalCounts], 
+  st_adata.obs["total_counts"][st_adata.obs["total_counts"] < histplotQCmaxTotalCounts],
   kde=True,
   bins=histplotQCbins,
   ax=axs[0, 1]
 ).set(title=f"Total counts < {histplotQCmaxTotalCounts}")
 p = sns.histplot(
-  st_adata.obs["n_genes_by_counts"], 
-  kde=True, 
-  bins=histplotQCbins, 
+  st_adata.obs["n_genes_by_counts"],
+  kde=True,
+  bins=histplotQCbins,
   ax=axs[1, 0]
 ).set(title=f"Genes by counts")
 p = sns.histplot(

docs/usage.md

@@ -141,7 +141,6 @@ The following parameters are exposed for preprocessing:
 - `--st_preprocess_min_counts`: Minimum number of counts for a spot to be considered in the analysis.
 - `--st_preprocess_min_genes`: Minimum number of genes expressed in a spot for the spot to be considered.
 - `--st_preprocess_min_cells`: Minimum number of spots expressing a gene for the gene to be considered.
-- `--st_preprocess_fig_size`: The figure size for the plots generated during preprocessing (_e.g._, quality control plots).
 - `--st_preprocess_hist_qc_max_total_counts`: Maximum total counts for the histogram plot in quality control.
 - `--st_preprocess_hist_qc_min_gene_counts`: Minimum gene counts for the histogram plot in quality control.
 - `--st_preprocess_hist_qc_bins`: Number of bins for the histogram plot in quality control.

modules/local/st_qc_and_normalisation.nf

@@ -38,7 +38,6 @@ process ST_QC_AND_NORMALISATION {
     quarto render ${report} \
         --output st_qc_and_normalisation.html \
         -P rawAdata:${st_raw} \
-        -P pltFigSize:${params.st_preprocess_fig_size} \
         -P minCounts:${params.st_preprocess_min_counts} \
         -P minGenes:${params.st_preprocess_min_genes} \
         -P minCells:${params.st_preprocess_min_cells} \

nextflow.config

@@ -18,7 +18,6 @@ params {
     spaceranger_save_reference   = false
 
     // Preprocessing, QC and normalisation
-    st_preprocess_fig_size                 = 6
     st_preprocess_min_counts               = 500
     st_preprocess_min_genes                = 250
     st_preprocess_min_cells                = 1

nextflow_schema.json

@@ -95,12 +95,6 @@
             "fa_icon": "fas fa-magnifying-glass-chart",
             "description": "Options related to the downstream analyses performed by the pipeline.",
             "properties": {
-                "st_preprocess_fig_size": {
-                    "type": "integer",
-                    "default": 6,
-                    "description": "The size of the QC figures, in inches.",
-                    "fa_icon": "fas fa-up-right-and-down-left-from-center"
-                },
                 "st_preprocess_min_counts": {
                     "type": "integer",
                     "default": 500,