update predicted accuracy name

maxibor · Jul 2, 2021 · e9bc4a8 · e9bc4a8
1 parent 80db47e
commit e9bc4a8
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/docs/source/output.md b/docs/source/output.md
@@ -7,7 +7,7 @@ The tabular outputs are  comma-separated file (`.csv`) with the following column
 ### `pydamage_results.csv` 
 
 * `reference`: name of the reference genome/contig
-* `pred_accuracy`: Predicted accuracy of Pydamage prediction, from the GLM modelling
+* `predicted_accuracy`: Predicted accuracy of Pydamage prediction, from the GLM modelling
 * `null_model_p0`: parameter `p0` of the null model
 * `null_model_p0_stdev`: standard error of the null model paramater `p0`
 * `damage_model_p`: parameter `p` of the damage model
@@ -27,7 +27,7 @@ The tabular outputs are  comma-separated file (`.csv`) with the following column
 
 ### `pydamage_filtered_results.csv` 
 
-Same file as above, but with contigs filtered with `qvalue <= 0.05` and `pred_accuracy >= threshold` with the filtering threshold determined with the [kneedle](https://ieeexplore.ieee.org/document/5961514) method.
+Same file as above, but with contigs filtered with `qvalue <= 0.05` and `predicted_accuracy >= threshold` with a user defined filtering threshold (default = 0.5), or determined with the [kneedle](https://ieeexplore.ieee.org/document/5961514) method.
 
 ### Plots
 

diff --git a/pydamage/filter.py b/pydamage/filter.py
@@ -13,7 +13,7 @@ def define_threshold(pydam_df, min_knee=0.5, alpha=0.05):
 
     Args:
         pydam_df (pandas df): pydamage results
-        min_knee (float, optional): Min pred_accuracy threshold.
+        min_knee (float, optional): Min predicted_accuracy threshold.
         alpha(float, optional): Alpha q-value threshold
     """
     thresholds = [i.round(2) for i in arange(min_knee, 1, 0.01)]
@@ -41,7 +41,7 @@ def filter_pydamage_results(pydam_df, acc_thresh, alpha=0.05):
 
     Args:
         pydam_df (pandas df): pydamage results
-        acc_thresh (float): predictiona accuracy threshold
+        acc_thresh (float): predicted accuracy threshold
         alpha (float, optional): Alpha q-value threshold. Defaults to 0.05.
     """
 
@@ -65,7 +65,7 @@ def apply_filter(csv, threshold, outdir, alpha=0.05):
         print(f"Optimal prediction accuracy threshold found to be: {threshold}")
     filt_df = filter_pydamage_results(df, acc_thresh=threshold)
     print(
-        f"Filtering PyDamage results with qvalue <= {alpha} and pred_accuracy >= {threshold}"
+        f"Filtering PyDamage results with qvalue <= {alpha} and predicted_accuracy >= {threshold}"
     )
     df_to_csv(filt_df, outdir, outfile)
     print(f"Filtered PyDamage results written to {outdir}/{outfile}")