Fixed some bugs in Manhattan plotting #47
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li-liwen
commented
Apr 17, 2022
li-liwen
commented
- Sorting problem when 'chr' column cannot be converted into numbers;
- Unable to change font name and size of tick labels;
- Unable to annotate all the dots higher than 'gwasp' when 'markernames' are set True
1. Sorting problem when chr column cannot be converted into numbers; 2. Unable to change font name and size of tick labels; 3. Unable to annote all the dots higher than gwasp when markernames=True
li-liwen
commented
Apr 17, 2022
| xycoords='data', xytext=(5, -15), textcoords='offset points', size=6, | ||
| bbox=dict(boxstyle="round", alpha=0.2), | ||
| arrowprops=dict(arrowstyle="wedge,tail_width=0.5", alpha=0.2, relpos=(0, 0))) | ||
| for j in range(len(df[chr].unique())): |
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This for-loop enables the annotator iterates all the chromosome, so that it won't only mark the first chromosome.
li-liwen
commented
Apr 17, 2022
| @@ -631,7 +634,7 @@ def mhat(df="dataframe", chr=None, pv=None, log_scale=True, color=None, dim=(6,4 | |||
| df['tpval'] = df[pv] | |||
| # df = df.sort_values(chr) | |||
| # if the column contains numeric strings | |||
| df = df.loc[pd.to_numeric(df[chr], errors='coerce').sort_values().index] | |||
| df = df.loc[pd.to_numeric(df[chr], errors='ignore').sort_values().index] | |||
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'coerce' will produce nan if not convertible, while ignore will maintain the input. This change from makes the column still sortable even if it cannot be converted to numbers. If the column isn't sorted, it will result in color problem in the plot.
li-liwen
commented
Apr 17, 2022
| @@ -681,7 +682,7 @@ def mhat(df="dataframe", chr=None, pv=None, log_scale=True, color=None, dim=(6,4 | |||
| else: | |||
| ylm = np.arange(0, max(df['tpval']+1), 1) | |||
| ax.set_yticks(ylm) | |||
| ax.set_xticklabels(xlabels, rotation=ar) | |||
| ax.set_xticklabels(xlabels, fontsize=axtickfontsize, fontproperties=axtickfontname, rotation=ar) | |||
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This enables the caller to change font name and font size of tick labels, which is especially useful when the labels is in another language.
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