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Further edits to plotter and misc_tools and plot_tools functions. Add…
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…ition of x_adjust to delta_text to allow all text to be moved by a user inputted amount
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@JAnns98
JAnns98 committed Oct 5, 2024
1 parent 9e3ec9e commit b613a2f
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Showing 6 changed files with 334 additions and 307 deletions.
8 changes: 5 additions & 3 deletions dabest/_effsize_objects.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1203,8 +1203,9 @@ def plot(
Pass relevant keyword arguments to the delta text. Pass any keyword arguments accepted by
matplotlib.text.Text here, as a string. If None, the following keywords are passed:
{"color": None, "alpha": 1, "fontsize": 10, "ha": 'center', "va": 'center', "rotation": 0,
"x_location": 'right', "x_coordinates": None, "y_coordinates": None}
Use "x_coordinates" and "y_coordinates" if you would like to specify the text locations manually.
"x_location": 'right', "x_coordinates": None, "y_coordinates": None, "x_adjust": 0}
Use "x_coordinates" and "y_coordinates" if you would like to specify the text locations manually.
Use "x_adjust" to adjust the x location of all the texts (positive moves right, negative left).
delta_dot : boolean, default True
Whether or not to display the delta dots on paired or repeated measure plots.
delta_dot_kwargs : dict, default None
Expand All @@ -1215,7 +1216,8 @@ def plot(
Whether or not to plot the effect size plot in a horizontal format.
horizontal_table_kwargs : dict, default None
Pass relevant keyword arguments to the horizontal table. If None, the following keywords are passed:
{'color' : 'yellow', 'alpha' :0.2, 'fontsize' : 12, 'text_color' : 'black', 'text_units' : None, 'paired_gap_dashes' : False, 'fontsize_label': 12}
{'color' : 'yellow', 'alpha' :0.2, 'fontsize' : 12, 'text_color' : 'black', 'text_units' : None,
'paired_gap_dashes' : False, 'fontsize_label': 12, 'label': 'Δ'}
Returns
-------
Expand Down
102 changes: 49 additions & 53 deletions dabest/misc_tools.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -321,7 +321,8 @@ def get_kwargs(plot_kwargs, ytick_color):
"rotation": 0,
"x_location": 'right',
"x_coordinates": None,
"y_coordinates": None
"y_coordinates": None,
"x_adjust": 0
}
if plot_kwargs["delta_text_kwargs"] is None:
delta_text_kwargs = default_delta_text_kwargs
Expand Down Expand Up @@ -366,7 +367,8 @@ def get_kwargs(plot_kwargs, ytick_color):
'text_color' : 'black',
'text_units' : None,
'paired_gap_dashes' : False,
'fontsize_label': 12
'fontsize_label': 12,
'label': 'Δ'
}
if plot_kwargs["horizontal_table_kwargs"] is None:
table_kwargs = default_table_kwargs
Expand Down Expand Up @@ -397,8 +399,6 @@ def get_color_palette(plot_kwargs, plot_data, xvar, show_pairs, idx, all_plot_gr
all_plot_groups : list
A list of all the group names.
"""


# Create color palette that will be shared across subplots.
color_col = plot_kwargs["color_col"]
if color_col is None:
Expand Down Expand Up @@ -550,6 +550,7 @@ def initialize_fig(plot_kwargs, dabest_obj, show_delta2, show_mini_meta, is_pair
if plot_kwargs["face_color"] is None:
face_color = "white"

# Create Figure and Axes
if fig_size is None:
all_groups_count = np.sum([len(i) for i in dabest_obj.idx])
# Increase the width (vertical layout) or height (horizontal layout) for delta-delta or mini-meta graph
Expand Down Expand Up @@ -638,6 +639,7 @@ def initialize_fig(plot_kwargs, dabest_obj, show_delta2, show_mini_meta, is_pair

contrast_axes = axins
rawdata_axes.contrast_axes = axins
table_axes = None

else:
# Here, we hardcode some figure parameters.
Expand Down Expand Up @@ -688,9 +690,7 @@ def initialize_fig(plot_kwargs, dabest_obj, show_delta2, show_mini_meta, is_pair
# Contrastplot ylim (Vertical) or xlim (Horizontal)
if horizontal or not float_contrast:
contrast_ylim, delta2_ylim = plot_kwargs["contrast_ylim"], plot_kwargs["delta2_ylim"]
if contrast_ylim is not None or (
delta2_ylim is not None and show_delta2
):
if contrast_ylim is not None or (delta2_ylim is not None and show_delta2):
if contrast_ylim is not None:
if delta2_ylim is not None and show_delta2:
if contrast_ylim != delta2_ylim:
Expand All @@ -717,9 +717,6 @@ def initialize_fig(plot_kwargs, dabest_obj, show_delta2, show_mini_meta, is_pair
else:
contrast_axes.set_ylim(contrast_ylim)




# Set raw axes y-label.
swarm_label = plot_kwargs["swarm_label"]
if swarm_label is None and yvar is None:
Expand Down Expand Up @@ -816,9 +813,11 @@ def get_plot_groups(is_paired, idx, proportional, all_plot_groups):
return temp_idx, temp_all_plot_groups


def add_counts_to_ticks(plot_data, xvar, yvar, rawdata_axes, plot_kwargs, horizontal=False):
def add_counts_to_ticks(plot_data, xvar, yvar, rawdata_axes, plot_kwargs, horizontal):
"""
Add the counts to the raw data axes labels.
Parameters
----------
plot_data : object (Dataframe)
Expand All @@ -831,7 +830,7 @@ def add_counts_to_ticks(plot_data, xvar, yvar, rawdata_axes, plot_kwargs, horizo
The raw data axes.
plot_kwargs : dict
Kwargs passed to the plot function.
horizontal : bool (default=False)
horizontal : bool
A boolean flag to determine if the plot is for horizontal plotting.
"""

Expand All @@ -850,33 +849,29 @@ def lookup_value(text):
pass
print(f"Key '{text}' not found in counts.")
return "N/A"

ticks_with_counts = []
if horizontal:
for yticklab in rawdata_axes.get_yticklabels():
t = yticklab.get_text()
te = t.split('\n')[-1] # Get the last line of the label
value = lookup_value(te)
ticks_with_counts.append(f"{t} (N={value})")

fontsize_rawxlabel = plot_kwargs.get("fontsize_rawxlabel")
rawdata_axes.set_yticklabels(ticks_with_counts, fontsize=fontsize_rawxlabel)

# Ensure ticks are at the correct locations
rawdata_axes.yaxis.set_major_locator(plt.FixedLocator(rawdata_axes.get_yticks()))
get_label, get_ticks = rawdata_axes.get_yticklabels, rawdata_axes.get_yticks
set_label, set_major_loc_method= rawdata_axes.set_yticklabels, rawdata_axes.yaxis.set_major_locator
else:
for xticklab in rawdata_axes.get_xticklabels():
t = xticklab.get_text()
te = t.split('\n')[-1] # Get the last line of the label
value = lookup_value(te)
ticks_with_counts.append(f"{t}\nN = {value}")

fontsize_rawxlabel = plot_kwargs.get("fontsize_rawxlabel")
rawdata_axes.set_xticklabels(ticks_with_counts, fontsize=fontsize_rawxlabel)
get_label, get_ticks = rawdata_axes.get_xticklabels, rawdata_axes.get_xticks
set_label, set_major_loc_method = rawdata_axes.set_xticklabels, rawdata_axes.xaxis.set_major_locator

for ticklab in get_label():
t = ticklab.get_text()
te = t.split('\n')[-1] # Get the last line of the label
value = lookup_value(te)
if horizontal:
ticks_with_counts.append(f"{t} (N={value})")
else:
ticks_with_counts.append(f"{t}\n(N={value})")

# Ensure ticks are at the correct locations
rawdata_axes.xaxis.set_major_locator(plt.FixedLocator(rawdata_axes.get_xticks()))
fontsize_rawxlabel = plot_kwargs.get("fontsize_rawxlabel")
set_label(ticks_with_counts, fontsize=fontsize_rawxlabel)

# Ensure ticks are at the correct locations
set_major_loc_method(plt.FixedLocator(get_ticks()))

def extract_contrast_plotting_ticks(is_paired, show_pairs, two_col_sankey, plot_groups, idx, sankey_control_group):
"""
Expand All @@ -897,7 +892,6 @@ def extract_contrast_plotting_ticks(is_paired, show_pairs, two_col_sankey, plot_
sankey_control_group : list
TBC.
"""

# Take note of where the `control` groups are.
ticks_to_skip_contrast = None
ticks_to_start_twocol_sankey = None
Expand Down Expand Up @@ -937,10 +931,11 @@ def extract_contrast_plotting_ticks(is_paired, show_pairs, two_col_sankey, plot_
ticks_to_plot = [
t for t in range(0, len(plot_groups)) if t not in ticks_to_skip
]

return ticks_to_skip, ticks_to_plot, ticks_to_skip_contrast, ticks_to_start_twocol_sankey

def set_xaxis_ticks_and_lims(show_delta2, show_mini_meta, rawdata_axes, contrast_axes, show_pairs, float_contrast,
ticks_to_skip, contrast_xtick_labels, plot_kwargs, horizontal=False):
ticks_to_skip, contrast_xtick_labels, plot_kwargs, horizontal):
"""
Set the x-axis/yaxis ticks and limits for the plotter function.
Expand All @@ -964,24 +959,26 @@ def set_xaxis_ticks_and_lims(show_delta2, show_mini_meta, rawdata_axes, contrast
A list of contrast xtick labels.
plot_kwargs : dict
Kwargs passed to the plot function.
horizontal : bool (default=False)
horizontal : bool
A boolean flag to determine if the plot is for horizontal plotting.
"""

if horizontal:
# Ticks
if show_delta2 is False and show_mini_meta is False:
contrast_axes.set_yticks(rawdata_axes.get_yticks())
else:
temp = rawdata_axes.get_yticks()
temp = np.append(temp, [max(temp) + 0, max(temp) + 1])
contrast_axes.set_yticks(temp)

# Lims
if show_pairs:
max_x = contrast_axes.get_ylim()[1]
rawdata_axes.set_ylim(-0.375, max_x)

if show_delta2 or show_mini_meta:
# Increase the xlim of raw data by 2
# Increase the ylim of raw data by 2
temp = rawdata_axes.get_ylim()
if show_pairs:
rawdata_axes.set_ylim(temp[0], temp[1] + 0.00)
Expand All @@ -992,13 +989,15 @@ def set_xaxis_ticks_and_lims(show_delta2, show_mini_meta, rawdata_axes, contrast
contrast_axes.set_ylim(rawdata_axes.get_ylim())

else:
# Ticks
if show_delta2 is False and show_mini_meta is False:
contrast_axes.set_xticks(rawdata_axes.get_xticks())
else:
temp = rawdata_axes.get_xticks()
temp = np.append(temp, [max(temp) + 1, max(temp) + 2])
contrast_axes.set_xticks(temp)

# Lims
if show_pairs:
max_x = contrast_axes.get_xlim()[1]
rawdata_axes.set_xlim(-0.375, max_x)
Expand All @@ -1020,11 +1019,8 @@ def set_xaxis_ticks_and_lims(show_delta2, show_mini_meta, rawdata_axes, contrast
for t in ticks_to_skip:
contrast_xtick_labels.insert(t, "")

if plot_kwargs["fontsize_contrastxlabel"] is not None:
fontsize_contrastxlabel = plot_kwargs["fontsize_contrastxlabel"]

contrast_axes.set_xticklabels(
contrast_xtick_labels, fontsize=fontsize_contrastxlabel
contrast_xtick_labels, fontsize=plot_kwargs["fontsize_contrastxlabel"]
)


Expand Down Expand Up @@ -1138,6 +1134,7 @@ def Gardner_Altman_Plot_Aesthetic_Adjustments(effect_size_type, plot_data, xvar,

og_ylim_raw = rawdata_axes.get_ylim()
og_xlim_raw = rawdata_axes.get_xlim()

# Normalize ylims and despine the floating contrast axes.
# Check that the effect size is within the swarm ylims.
if effect_size_type in ["mean_diff", "cohens_d", "hedges_g", "cohens_h"]:
Expand Down Expand Up @@ -1286,7 +1283,7 @@ def Gardner_Altman_Plot_Aesthetic_Adjustments(effect_size_type, plot_data, xvar,

def Cumming_Plot_Aesthetic_Adjustments(contrast_axes, reflines_kwargs, is_paired, show_pairs, two_col_sankey, idx, ticks_to_start_twocol_sankey,
proportional, ticks_to_skip, temp_idx, rawdata_axes, redraw_axes_kwargs, ticks_to_skip_contrast,
show_delta2, show_mini_meta, horizontal=False):
show_delta2, show_mini_meta, horizontal):

"""
Aesthetic adjustments for the Cumming plot.
Expand Down Expand Up @@ -1323,10 +1320,11 @@ def Cumming_Plot_Aesthetic_Adjustments(contrast_axes, reflines_kwargs, is_paired
A boolean flag to determine if the plot will have a delta-delta effect size.
show_mini_meta : bool
A boolean flag to determine if the plot will have a mini-meta effect size.
horizontal : bool (default=False)
horizontal : bool
A boolean flag to determine if the plot is for horizontal plotting.
"""


# If 0 lies within the ylim of the contrast axes, draw a zero reference line.
if horizontal:
contrast_axes_lim = contrast_axes.get_xlim()
Expand All @@ -1343,7 +1341,7 @@ def Cumming_Plot_Aesthetic_Adjustments(contrast_axes, reflines_kwargs, is_paired
if contrast_lim_low < 0 < contrast_lim_high:
method(0, **reflines_kwargs)

# Add spine lines to link the relevant groups in the plot. (re-add as we removed spines)
# Add axes spine lines to link the relevant groups in the plot. (re-add as we removed spines)
if horizontal:
if two_col_sankey:
rightend_ticks = np.array([len(i) - 2 for i in idx]) + np.array(ticks_to_start_twocol_sankey)
Expand All @@ -1360,7 +1358,7 @@ def Cumming_Plot_Aesthetic_Adjustments(contrast_axes, reflines_kwargs, is_paired

for ax in [rawdata_axes]:
sns.despine(ax=ax, left=True)
xlim = ax.get_xlim()
xlim, ylim = ax.get_xlim(), ax.get_ylim()
redraw_axes_kwargs["x"] = xlim[0]
for k, start_tick in enumerate(starting_ticks):
end_tick = rightend_ticks[k]
Expand All @@ -1370,6 +1368,7 @@ def Cumming_Plot_Aesthetic_Adjustments(contrast_axes, reflines_kwargs, is_paired
**redraw_axes_kwargs
)
ax.set_xlim(xlim)
ax.set_ylim(ylim)
del redraw_axes_kwargs["x"]

# Remove y ticks and labels from the contrast axes.
Expand Down Expand Up @@ -1400,7 +1399,7 @@ def Cumming_Plot_Aesthetic_Adjustments(contrast_axes, reflines_kwargs, is_paired
[rightend_ticks_raw, rightend_ticks_contrast],
):
sns.despine(ax=ax, bottom=True)
ylim = ax.get_ylim()
xlim, ylim = ax.get_xlim(), ax.get_ylim()
redraw_axes_kwargs["y"] = ylim[0]
for k, start_tick in enumerate(starting_ticks_current):
end_tick = rightend_ticks_current[k]
Expand All @@ -1409,6 +1408,7 @@ def Cumming_Plot_Aesthetic_Adjustments(contrast_axes, reflines_kwargs, is_paired
xmax=end_tick,
**redraw_axes_kwargs
)
ax.set_xlim(xlim)
ax.set_ylim(ylim)
del redraw_axes_kwargs["y"]

Expand All @@ -1427,11 +1427,7 @@ def Cumming_Plot_Aesthetic_Adjustments(contrast_axes, reflines_kwargs, is_paired
rawdata_axes.set_ylim(swarm_ylim[1], swarm_ylim[0])
contrast_axes.set_ylim(contrast_ylim[1], contrast_ylim[0])

# Modification to reset xlim for vertical plots -> otherwise barplots swarms and contrast are misaligned... to be fixed
if not horizontal:
rawdata_axes.set_xlim(contrast_axes.get_xlim())

def Redraw_Spines(rawdata_axes, contrast_axes, redraw_axes_kwargs, float_contrast, horizontal=False):
def Redraw_Spines(rawdata_axes, contrast_axes, redraw_axes_kwargs, float_contrast, horizontal):
"""
Aesthetic general adjustments across both GA and Cumming plots.
Expand All @@ -1447,7 +1443,7 @@ def Redraw_Spines(rawdata_axes, contrast_axes, redraw_axes_kwargs, float_contras
Kwargs passed to the plot function.
float_contrast : bool
A boolean flag to determine if the plot is GA or Cum
horizontal : bool (default=False)
horizontal : bool
A boolean flag to determine if the plot is for horizontal plotting.
"""

Expand Down
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