diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py
index 1ad1f456..ff89d889 100644
--- a/bin/coverage_report_single.py
+++ b/bin/coverage_report_single.py
@@ -106,7 +106,7 @@ def load_files(self, threshold, exon_stats,
# format according to output of
# https://github.com/eastgenomics/eggd_generate_bed
panel_name = panel_name.replace("_", " ").strip()
- panel_name = panel_name.replace("&", ", ")
+ panel_name = panel_name.replace("&", ",  ")
panel = "
Panel(s) / gene(s) included in report: {}\
".format(panel_name)
@@ -721,7 +721,7 @@ def summary_gene_plot(self, cov_summary, threshold):
cov_summary = cov_summary.sort_values(by=[threshold], ascending=False)
- summary_plot, axs = plt.subplots(figsize=(18, 7.5))
+ summary_plot, axs = plt.subplots(figsize=(22, 7.5))
plt.bar(
cov_summary["gene"], [int(x) for x in cov_summary[threshold]],
color=cov_summary.colours
@@ -736,11 +736,15 @@ def summary_gene_plot(self, cov_summary, threshold):
# plot formatting
axs.tick_params(labelsize=6, length=0)
- plt.xticks(rotation=35, color="#565656")
+ plt.xticks(rotation=55, color="#565656")
+
+ # adjust whole plot marins
+ axs.margins(x=0.01)
+ axs.autoscale_view(scaley=True)
vals = np.arange(0, 110, 10).tolist()
plt.yticks(vals, vals)
- axs.tick_params(axis='both', which='major', labelsize=10)
+ axs.tick_params(axis='both', which='major', labelsize=8)
plt.xlabel("")
plt.ylabel("% coverage ({})".format(threshold), fontsize=11)
@@ -872,7 +876,7 @@ def generate_report(self, cov_stats, cov_summary, snps_low_cov,
sub_threshold_stats = sub_threshold_stats.rename(columns={
"gene": "Gene",
"tx": "Transcript",
- "chrom": "Chromosome",
+ "chrom": "Chr",
"exon": "Exon",
"exon_len": "Length",
"exon_start": "Start",
@@ -894,7 +898,7 @@ def generate_report(self, cov_stats, cov_summary, snps_low_cov,
total_stats = total_stats.rename(columns={
"gene": "Gene",
"tx": "Transcript",
- "chrom": "Chromosome",
+ "chrom": "Chr",
"exon": "Exon",
"exon_len": "Length",
"exon_start": "Start",