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Add top ticks to plots #118

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39d3ef7
feat: Ensure maximum y-value is included as a tick in modification fr…
Colelyman Apr 3, 2025
621e2a5
Remove comments and check for y_max as last value
Colelyman Apr 3, 2025
19ef913
feat: Ensure maximum y-axis tick value is included in plot_indel_size…
Colelyman Apr 3, 2025
40af728
feat: Ensure maximum y-axis value is included in frameshift plot labels
Colelyman Apr 3, 2025
dfe4fd1
refactor: Improve y-axis label generation in plot_quantification_wind…
Colelyman Apr 3, 2025
ef02afa
Extract calculating y label values into a function
Colelyman Apr 3, 2025
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78 changes: 38 additions & 40 deletions CRISPResso2/CRISPRessoPlot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,6 +72,7 @@ def get_nuc_color(nuc, alpha):

return (charSum, (1-charSum), (2*charSum*(1-charSum)))


def get_color_lookup(nucs, alpha, custom_colors=None):
if custom_colors is None:
colorLookup = {}
Expand All @@ -95,6 +96,18 @@ def hex_to_rgb(value):
lv = len(value)
return tuple(int(value[i:i + lv // 3], 16) for i in range(0, lv, lv // 3))


def get_y_label_values(y_max, round=False, num_ticks=6):
"""Get y label values that are evenly spaced."""
y_label_values = np.arange(0, 1, 1.0 / 6.0)
if y_max > 0:
y_label_values = np.linspace(0, y_max, num_ticks).astype(int)
y_label_values[-1] = int(y_max)
if round:
y_label_values = np.round(y_label_values)
return y_label_values


def plot_nucleotide_quilt(nuc_pct_df,mod_pct_df,fig_filename_root, custom_colors, save_also_png=False,sgRNA_intervals=None,min_text_pct=0.5,max_text_pct=0.95,quantification_window_idxs=None,sgRNA_names=None,sgRNA_mismatches=None,shade_unchanged=True,group_column='Batch', **kwargs):
"""
Plots a nucleotide quilt with each square showing the percentage of each base at that position in the reference
Expand Down Expand Up @@ -347,9 +360,8 @@ def plot_indel_size_distribution(
ax.set_xlim([xmin, xmax])
ax.set_title(title)
ax.set_ylabel('Sequences % (no.)')
y_label_values = np.round(
np.linspace(0, min(100, max(ax.get_yticks())), 6),
)
max_y = min(100, max(ax.get_yticks()))
y_label_values = get_y_label_values(max_y, round=True)
ax.set_yticks(y_label_values)
ax.set_yticklabels([
'%.1f%% (%.0f)' % (pct, pct / 100 * n_this_category)
Expand Down Expand Up @@ -427,9 +439,8 @@ def plot_frequency_deletions_insertions(
lgd.legend_handles[1].set_height(6)

ax.set_xlim([-1, xmax_ins])
y_label_values= np.round(
np.linspace(0, min(counts_total, max(ax.get_yticks())), 6),
)
max_y = min(counts_total, max(ax.get_yticks()))
y_label_values = get_y_label_values(max_y, round=True)
ax.set_yticks(y_label_values)
ax.set_yticklabels(
[
Expand Down Expand Up @@ -466,9 +477,8 @@ def plot_frequency_deletions_insertions(
lgd.legend_handles[1].set_height(6)

ax.set_xlim([-1 * xmax_del, 1])
y_label_values = np.round(
np.linspace(0, min(counts_total, max(ax.get_yticks())), 6),
)
y_max = min(counts_total, max(ax.get_yticks()))
y_label_values = get_y_label_values(y_max, round=True)
ax.set_yticks(y_label_values)
ax.set_yticklabels(
[
Expand Down Expand Up @@ -505,9 +515,8 @@ def plot_frequency_deletions_insertions(
lgd.legend_handles[1].set_height(6)

ax.set_xlim([-1, xmax_mut])
y_label_values= np.round(
np.linspace(0, min(counts_total, max(ax.get_yticks())), 6),
)
y_max = min(counts_total, max(ax.get_yticks()))
y_label_values = get_y_label_values(y_max, round=True)
ax.set_yticks(y_label_values)
ax.set_yticklabels(
[
Expand Down Expand Up @@ -631,9 +640,7 @@ def plot_amplicon_modifications(
fancybox=True,
shadow=True,
)
y_label_values = np.arange(0, 1, 1.0 / 6.0)
if y_max > 0:
y_label_values = np.arange(0, y_max, y_max / 6.0)
y_label_values = get_y_label_values(y_max, round=True)
if num_refs == 1:
ax.set_ylabel('Sequences: % Total ( no. )')
ax.set_yticks(y_label_values)
Expand Down Expand Up @@ -793,9 +800,7 @@ def plot_modification_frequency(
fancybox=True,
shadow=True,
)
y_label_values = np.arange(0, 1, 1.0 / 6.0)
if y_max > 0:
y_label_values = np.arange(0, y_max, y_max / 6.0)
y_label_values = get_y_label_values(y_max)
ax.set_xticks(np.arange(
0,
ref_len,
Expand Down Expand Up @@ -958,9 +963,7 @@ def plot_quantification_window_locations(
fancybox=True,
shadow=True,
)
y_label_values = np.arange(0, 1, 1.0 / 6.0)
if y_max > 0:
y_label_values = np.arange(0, y_max, y_max / 6.0).astype(int)
y_label_values = get_y_label_values(y_max)
ax.set_yticks(y_label_values)
ax.set_yticklabels(
[
Expand Down Expand Up @@ -1244,10 +1247,7 @@ def plot_global_modifications_reference(
fancybox=True,
shadow=True,
)
y_label_values = np.arange(0, 1, 1.0 / 6.0)
if y_max > 0:
y_label_values = np.arange(0, y_max, y_max / 6.0).astype(int)

y_label_values = get_y_label_values(y_max)
ax.set_ylabel('Sequences: % Total ( no. )')
ax.set_yticks(y_label_values)
ax.set_yticklabels(
Expand Down Expand Up @@ -1473,9 +1473,7 @@ def plot_frameshift_frequency(
ax1.tick_params(axis='both', which='major', labelsize=24)
ax1.tick_params(axis='both', which='minor', labelsize=24)
ax1.set_ylabel('Sequences % (no.)')
y_label_values = np.round(
np.linspace(0, min(100, max(ax1.get_yticks())), 6),
)
y_label_values = get_y_label_values(max_y, round=True)
ax1.set_yticks(y_label_values)
ax1.set_yticklabels(
[
Expand Down Expand Up @@ -1512,9 +1510,8 @@ def plot_frameshift_frequency(
)
ax2.set_title(plot_titles['if'])
ax2.set_ylabel('Sequences % (no.)')
y_label_values = np.round(
np.linspace(0, min(100, max(ax2.get_yticks())), 6),
)
max_y = min(100, max(ax2.get_yticks()))
y_label_values = get_y_label_values(max_y, round=True)
ax2.set_yticks(y_label_values)
ax2.set_yticklabels(
[
Expand Down Expand Up @@ -1608,9 +1605,8 @@ def plot_global_frameshift_in_frame_mutations(
ax1.tick_params(axis='both', which='minor', labelsize=24)
ax1.tick_params(left=True, bottom=True)
ax1.set_ylabel('Sequences % (no.)')
y_label_values = np.round(np.linspace(
0, min(100, max(ax1.get_yticks())), 6),
)
y_max = min(100, max(ax1.get_yticks()))
y_label_values = get_y_label_values(y_max, round=True)
ax1.set_yticks(y_label_values)
ax1.set_yticklabels(
[
Expand Down Expand Up @@ -1648,9 +1644,8 @@ def plot_global_frameshift_in_frame_mutations(
)
ax2.set_title('Global In-frame profile')
ax2.set_ylabel('Sequences % (no.)')
y_label_values = np.round(np.linspace(
0, min(100, max(ax2.get_yticks())), 6,
))
y_max = min(100, max(ax2.get_yticks()))
y_label_values = get_y_label_values(y_max, round=True)
ax2.set_yticks(y_label_values)
ax2.set_yticklabels(
[
Expand Down Expand Up @@ -2254,7 +2249,8 @@ def plot_subs_across_ref(ref_len, ref_seq, ref_name, ref_count, all_substitution
# lgd=ax.legend(legend_patches,legend_labels,ncol=1)
lgd = ax.legend(handles=legend_patches, labels=legend_labels, loc='upper center', bbox_to_anchor=(0.3, -0.15), ncol=2, fancybox=True, shadow=True)

y_label_values= np.round(np.linspace(0, max(y_max, min(max(tots), max(ax.get_yticks()))), 6))# np.arange(0,y_max,y_max/6.0)
max_y = max(y_max, min(max(tots), max(ax.get_yticks())))
y_label_values = get_y_label_values(max_y, round=True)
ax.set_yticks(y_label_values)
ax.set_yticklabels(
[
Expand Down Expand Up @@ -3575,7 +3571,8 @@ def plot_read_barplot(N_READS_INPUT, N_READS_AFTER_PREPROCESSING, N_TOTAL,
ax.set_xticks(np.arange(len(sizes)))
ax.set_xticklabels(labels)
ax.set_ylabel('Sequences % (no.)')
y_label_values = np.round(np.linspace(0, max(N_READS_INPUT, max(ax.get_yticks())), 6))
y_max = max(N_READS_INPUT, max(ax.get_yticks()))
y_label_values = get_y_label_values(y_max, round=True)

ax.set_yticks(y_label_values)
ax.set_yticklabels(['%.1f%% (%.0f)' % (100*cnt/N_READS_INPUT, cnt) for cnt in y_label_values])
Expand Down Expand Up @@ -3670,7 +3667,8 @@ def plot_class_piechart_and_barplot(class_counts_order, class_counts, ref_names,
ax.set_xticklabels(labels)
ax.set_xticklabels([X.replace("&", " & ").replace("_UNMODIFIED", " UNMODIFIED").replace("_MODIFIED", " MODIFIED") for X in labels])
ax.set_ylabel('Sequences % (no.)')
y_label_values = np.round(np.linspace(0, min(100, max(ax.get_yticks())), 6))
y_max = min(100, max(ax.get_yticks()))
y_label_values = get_y_label_values(y_max, round=True)
ax.set_yticks(y_label_values)
ax.set_yticklabels(['%.1f%% (%.0f)' % (pct, pct/100*N_TOTAL) for pct in y_label_values])
#if too many barplots, flip the labels
Expand Down
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