Update VolcanoPlot props #554
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -21,7 +21,6 @@ def VolcanoPlot( | |
| gene='GENE', | ||
| annotation=None, | ||
| logp=True, | ||
| xlabel=None, | ||
| ylabel='-log10(p)', | ||
| point_size=5, | ||
|
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@@ -33,7 +32,8 @@ def VolcanoPlot( | |
| genomewideline_color='grey', | ||
| genomewideline_width=1, | ||
| highlight=True, | ||
| highlight_color="red", | ||
| **kwargs | ||
| ): | ||
| """Return a Dash Bio VolcanoPlot figure. | ||
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@@ -72,7 +72,6 @@ def VolcanoPlot( | |
| plotting the raw value could be useful for other genome-wide plots | ||
| (e.g., peak heights, Bayes factors, test statistics, and other | ||
| "scores"). | ||
| - xlabel (string; optional): Label of the x axis. | ||
| - ylabel (string; default '-log10(p)'): Label of the y axis. | ||
| - point_size (number; default 5): Size of the points of the Scatter | ||
|
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@@ -110,11 +109,29 @@ def VolcanoPlot( | |
| dataframe = pd.DataFrame( | ||
| np.random.randint(0,100,size=(100, 2)), | ||
| columns=['P', 'EFFECTSIZE']) | ||
| fig = create_volcano(dataframe, title=dict(text='XYZ Volcano plot')) | ||
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| plotly.offline.plot(fig, image='png') | ||
| ''' | ||
| - Additional keys (misc.): Arbitrary arguments can be passed to modify the | ||
| Layout and styling of the graph. A full reference of acceptable args is | ||
| available [here](https://plotly.com/python-api-reference/generated/plotly.graph_objects | ||
| .Layout.html). | ||
|
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||
| Some commonly used layout keys are: | ||
| - title (dict: optional): Dict with compatible properties for the title of | ||
| the figure layout. | ||
| - xaxis (dict: optional): Dict with compatible properties for the x-axis of | ||
| the figure layout. | ||
| - yaxis (dict: optional): Dict with compatible properties for the y-axis of | ||
| the figure layout. | ||
| - height (number; optional): Sets the plot's height (in px). | ||
| - width (number; optional): Sets the plot's width (in px). | ||
| - margin (dict | plotly.graph_objects.layout.Margin instance): A dict or Margin | ||
| instance that sets the separation between the main plotting space and | ||
| the outside of the figure. | ||
| - legend (dict | plotly.graph_objects.layout.Legend instance): A dict or Legend | ||
| instance with compatible properties. | ||
| """ | ||
|
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| vp = _VolcanoPlot( | ||
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@@ -128,7 +145,6 @@ def VolcanoPlot( | |
| ) | ||
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| return vp.figure( | ||
| xlabel=xlabel, | ||
| ylabel=ylabel, | ||
| point_size=point_size, | ||
|
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@@ -140,7 +156,8 @@ def VolcanoPlot( | |
| genomewideline_color=genomewideline_color, | ||
| genomewideline_width=genomewideline_width, | ||
| highlight=highlight, | ||
| highlight_color=highlight_color, | ||
| **kwargs | ||
| ) | ||
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@@ -274,7 +291,6 @@ def __init__( | |
|
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| def figure( | ||
| self, | ||
| xlabel=None, | ||
| ylabel='-log10(p)', | ||
| point_size=5, | ||
|
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@@ -287,14 +303,13 @@ def figure( | |
| genomewideline_width=1, | ||
| highlight=True, | ||
| highlight_color='red', | ||
| **kwargs | ||
| ): | ||
| """Return a figure object compatible with plotly.graph_objects. | ||
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||
| Keyword arguments: | ||
| - xlabel (string; optional): Label of the x-axis. | ||
| - ylabel (string; default '-log10(p)'): Label of the y-axis. | ||
| - point_size (number; default 5): Size of the points of the scatter | ||
| plot. | ||
| - col (string; optional): Color of the points of the Scatter plot. Can | ||
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@@ -322,6 +337,25 @@ def figure( | |
| - highlight_color (string; default 'red'): Color of the data points | ||
| highlighted because considered significant. Can be in any color | ||
| format accepted by plotly.graph_objects. | ||
| - Additional keys (misc.): Arbitrary arguments can be passed to modify the | ||
| Layout and styling of the graph. A full reference of acceptable args is | ||
| available [here](https://plotly.com/python-api-reference/generated/plotly.graph_objects | ||
| .Layout.html). | ||
|
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||
| Some commonly used layout keys are: | ||
| - title (dict: optional): Dict with compatible properties for the title of | ||
| the figure layout. | ||
| - xaxis (dict: optional): Dict with compatible properties for the x-axis of | ||
| the figure layout. | ||
| - yaxis (dict: optional): Dict with compatible properties for the y-axis of | ||
| the figure layout. | ||
| - height (number; optional): Sets the plot's height (in px). | ||
| - width (number; optional): Sets the plot's width (in px). | ||
| - margin (dict | plotly.graph_objects.layout.Margin instance): A dict or Margin | ||
| instance that sets the separation between the main plotting space and | ||
| the outside of the figure. | ||
| - legend (dict | plotly.graph_objects.layout.Legend instance): A dict or Legend | ||
| instance with compatible properties. | ||
| """ | ||
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| if xlabel is None: | ||
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@@ -355,13 +389,18 @@ def figure( | |
| col = 'black' | ||
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| layout = go.Layout( | ||
| title={'text': 'Volcano Plot', | ||
|
There was a problem hiding this comment. Should we be using the Alternatively we could drop So yeah, I guess my inclination is to drop There was a problem hiding this comment. Dropped in 3e2ce66. |
||
| 'font': {'family': 'sans-serif', 'size': 20}, | ||
| 'x': 0.5, | ||
| 'xanchor': 'right', | ||
| 'yanchor': 'top' | ||
| }, | ||
| hovermode='closest', | ||
| legend={'bgcolor': '#ebf1fa', | ||
| 'yanchor': 'top', | ||
| 'x': 1.01, | ||
| "font": {"family": "sans-serif"} | ||
| }, | ||
| xaxis={ | ||
| 'title': xlabel, | ||
| 'zeroline': False, | ||
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@@ -373,6 +412,8 @@ def figure( | |
| } | ||
| ) | ||
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| layout.update(**kwargs) | ||
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| data_to_plot = [] # To contain the data traces | ||
| tmp = pd.DataFrame() # Empty DataFrame to contain the highlighted data | ||
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Since we're accepting
**kwargshere and passing them togo.Layout, do we actually need any of the other args you're adding here? We can list some of the common ones (including the ones you're including explicitly now) in the description here, they'd all work identically as part of kwargs.x_axisandy_axis: in the docstring there's no_and I'd argue it's cleaner without, then these can just be left to kwargs as well.In order to keep the defaults you have but allow users to update the layout arbitrarily with kwargs after that, I suspect the easiest would be to generate the default layout first, then do
layout.update(**kwargs). A little exploring shows that this does a deep merge, so if your kwargs are justxaxis=dict(color="red")you'll still get the rest of the x axis as set in the default layout.There was a problem hiding this comment.
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I thought it might be nice to have the most commonly used args available explicitly, especially for users that use IDE's which show parameter info, but simply including them as part of the documentation is also an option. However, retaining them as explicit args would also potentially save users a trip to the Plotly graphing library docs (unless we also update dash-docs with some better examples). I think it's a trade-off between cleaner params (with everything as kwargs) and easier "default" use of the component.
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Fair point re: IDE docs & completion. That said for everything except
heightandwidthyou're still going to need to visit the graphing library docs to find out what goes inside the object, and it feels a bit arbitrary to be pulling in just a few layout options - as if the ones in kwargs are less-fully-supported or something. So I still think we'll be better off removing all of them and just documenting a few (the set you've proposed adding here looks good) in the docstring.There was a problem hiding this comment.
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That's a great point - Updated in a5b996a.