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Fixed a bug when loading feature names and also limit plot xaxis to a… #14

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Feb 15, 2022
Merged

Fixed a bug when loading feature names and also limit plot xaxis to a… #14

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5 changes: 3 additions & 2 deletions filter_chimeric_reads
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Original file line number Diff line number Diff line change
Expand Up @@ -33,14 +33,15 @@ def generate_umi_count_plot(count_vec, count_threshold, output_file):
background = plt.bar(count_vec.index[~idx], count_vec.values[~idx], linewidth = 0, color = 'blue')
signal = plt.bar(count_vec.index[idx], count_vec.values[idx], linewidth = 0, color = 'red')
plt.legend([background, signal], ["background", "signal"], loc = 'upper right')
plt.xlim(0, count_vec.index.max() + 1)
plt.xlim(0, min(count_vec.index.max() + 1, 50))
plt.xlabel('UMI with certain number of reads')
plt.ylabel('Number of UMIs')
plt.savefig(output_file, dpi = 500)
plt.close()

def load_feature_names(feature_file):
return pd.read_csv(feature_file, header = None, index_col = 0, squeeze = True).values
df = pd.read_csv(feature_file, header = None, index_col = 0)
return df[df.columns[0]].values

def write_csv(new_barcodes, feature_names, tot_umis, output_file):
with open(output_file, 'w') as fout:
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