A Python package to make publicationready but customizable forest plots.
Project description
Forestplot
Easy API for forest plots.
A Python package to make publicationready but customizable forest plots.
This package makes publicationready forest plots easy to make outofthebox. Users provide a dataframe
(e.g. from a spreadsheet) where rows correspond to a variable/study with columns including estimates, variable labels, and lower and upper confidence interval limits.
Additional options allow easy addition of columns in the dataframe
as annotations in the plot.
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Installation
pip install forestplot
conda install forestplot
git clone https://github.com/LSYS/forestplot.git
cd forestplot
pip install .
Developer installation
git clone https://github.com/LSYS/forestplot.git
cd forestplot
pip install r requirements_dev.txt
make lint
make test
Quick Start
import forestplot as fp
df = fp.load_data("sleep") # companion example data
df.head(3)
var  r  moerror  label  group  ll  hl  n  power  pval  

0  age  0.0903729  0.0696271  in years  age  0.02  0.16  706  0.671578  0.0163089 
1  black  0.0270573  0.0770573  =1 if black  other factors  0.1  0.05  706  0.110805  0.472889 
2  clerical  0.0480811  0.0719189  =1 if clerical worker  occupation  0.03  0.12  706  0.247768  0.201948 
(* This is a toy example of how certain factors correlate with the amount of sleep one gets. See the notebook that generates the data.)
The example input dataframe above have 4 key columns
Column  Description  Required 

var 
Variable label  ✓ 
r 
Correlation coefficients (estimates to plot)  ✓ 
label 
Variable labels  ✓ 
group 
Variable grouping labels  
ll 
Conf. int. lower limits  
hl 
Containing the conf. int. higher limits  
n 
Sample size  
power 
Statistical power  
pval 
Pvalue 
(See Gallery and API Options for more details on required and optional arguments.)
Make the forest plot
fp.forestplot(df, # the dataframe with results data
estimate="r", # col containing estimated effect size
ll="ll", hl="hl", # columns containing conf. int. lower and higher limits
varlabel="label", # column containing variable label
ylabel="Confidence interval", # ylabel title
xlabel="Pearson correlation", # xlabel title
)
Save the plot
plt.savefig("plot.png", bbox_inches="tight")
Some Examples With Customizations
 Add variable groupings, add group order, and sort by estimate size.
fp.forestplot(df, # the dataframe with results data
estimate="r", # col containing estimated effect size
moerror="moerror", # columns containing conf. int. margin of error
varlabel="label", # column containing variable label
capitalize="capitalize", # Capitalize labels
groupvar="group", # Add variable groupings
# group ordering
group_order=["labor factors", "occupation", "age", "health factors",
"family factors", "area of residence", "other factors"],
sort=True, # sort in ascending order (sorts within group if group is specified)
)
 Add pvalues on the right and color alternate rows gray
fp.forestplot(df, # the dataframe with results data
estimate="r", # col containing estimated effect size
ll="ll", hl="hl", # columns containing conf. int. lower and higher limits
varlabel="label", # column containing variable label
capitalize="capitalize", # Capitalize labels
groupvar="group", # Add variable groupings
# group ordering
group_order=["labor factors", "occupation", "age", "health factors",
"family factors", "area of residence", "other factors"],
sort=True, # sort in ascending order (sorts within group if group is specified)
pval="pval", # Column of pvalue to be reported on right
color_alt_rows=True, # Gray alternate rows
ylabel="Est.(95% Conf. Int.)", # ylabel to print
**{"ylabel1_size": 11} # control size of printed ylabel
)
 Customize annotations and make it a table
fp.forestplot(df, # the dataframe with results data
estimate="r", # col containing estimated effect size
ll="ll", hl="hl", # lower & higher limits of conf. int.
varlabel="label", # column containing the varlabels to be printed on far left
capitalize="capitalize", # Capitalize labels
pval="pval", # column containing pvalues to be formatted
annote=["n", "power", "est_ci"], # columns to report on left of plot
annoteheaders=["N", "Power", "Est. (95% Conf. Int.)"], # ^corresponding headers
rightannote=["formatted_pval", "group"], # columns to report on right of plot
right_annoteheaders=["Pvalue", "Variable group"], # ^corresponding headers
xlabel="Pearson correlation coefficient", # xlabel title
table=True, # Format as a table
)
 Strip down all bells and whistle
fp.forestplot(df, # the dataframe with results data
estimate="r", # col containing estimated effect size
ll="ll", hl="hl", # lower & higher limits of conf. int.
varlabel="label", # column containing the varlabels to be printed on far left
capitalize="capitalize", # Capitalize labels
ci_report=False, # Turn off conf. int. reporting
flush=False, # Turn off leftflush of text
**{'fontfamily': 'sansserif'} # revert to sansserif
)
 Example with more customizations
fp.forestplot(df, # the dataframe with results data
estimate="r", # col containing estimated effect size
ll="ll", hl="hl", # lower & higher limits of conf. int.
varlabel="label", # column containing the varlabels to be printed on far left
capitalize="capitalize", # Capitalize labels
pval="pval", # column containing pvalues to be formatted
annote=["n", "power", "est_ci"], # columns to report on left of plot
annoteheaders=["N", "Power", "Est. (95% Conf. Int.)"], # ^corresponding headers
rightannote=["formatted_pval", "group"], # columns to report on right of plot
right_annoteheaders=["Pvalue", "Variable group"], # ^corresponding headers
groupvar="group", # column containing group labels
group_order=["labor factors", "occupation", "age", "health factors",
"family factors", "area of residence", "other factors"],
xlabel="Pearson correlation coefficient", # xlabel title
xticks=[.4,.2,0, .2], # xticks to be printed
sort=True, # sort estimates in ascending order
table=True, # Format as a table
# Additional kwargs for customizations
**{"marker": "D", # set maker symbol as diamond
"markersize": 35, # adjust marker size
"xlinestyle": (0, (10, 5)), # long dash for xreference line
"xlinecolor": "#808080", # gray color for xreference line
"xtick_size": 12, # adjust xticker fontsize
}
)
Annotations arguments allowed include:
ci_range
: Confidence interval range (e.g.(0.39 to 0.25)
).est_ci
: Estimate and CI (e.g.0.32(0.39 to 0.25)
).formatted_pval
: Formatted pvalues (e.g.0.01**
).
To confirm what processed columns
are available as annotations, you can do:
processed_df, ax = fp.forestplot(df,
... # other arguments here
return_df=True # return processed dataframe with processed columns
)
processed_df.head(3)
label  group  n  r  CI95%  pval  BF10  power  var  hl  ll  moerror  formatted_r  formatted_ll  formatted_hl  ci_range  est_ci  formatted_pval  formatted_n  formatted_power  formatted_est_ci  yticklabel  formatted_formatted_pval  formatted_group  yticklabel2  

0  Mins worked per week  Labor factors  706  0.321384  [0.39 0.25]  1.99409e18  1.961e+15  1  totwrk  0.25  0.39  0.0686165  0.32  0.39  0.25  (0.39 to 0.25)  0.32(0.39 to 0.25)  0.0***  706  1  0.32(0.39 to 0.25)  Mins worked per week 706 1.0 0.32(0.39 to 0.25)  0.0***  Labor factors  0.0*** Labor factors 
1  Years of schooling  Labor factors  706  0.0950039  [0.17 0.02]  0.0115515  1.137  0.72  educ  0.02  0.17  0.0749961  0.1  0.17  0.02  (0.17 to 0.02)  0.10(0.17 to 0.02)  0.01**  706  0.72  0.10(0.17 to 0.02)  Years of schooling 706 0.72 0.10(0.17 to 0.02)  0.01**  Labor factors  0.01** Labor factors 
Gallery and API Options
Check out this jupyter notebook for a gallery variations of forest plots possible outofthebox. The table below shows the list of arguments users can pass in. More finedgrained control for base plot options (eg font sizes, marker colors) can be inferred from the example notebook gallery.
Option  Description  Required 

dataframe 
Pandas dataframe where rows are variables (or studies for metaanalyses) and columns include estimated effect sizes, labels, and confidence intervals, etc.  ✓ 
estimate 
Name of column in dataframe containing the estimates. 
✓ 
varlabel 
Name of column in dataframe containing the variable labels (study labels if metaanalyses). 
✓ 
ll 
Name of column in dataframe containing the conf. int. lower limits. 

hl 
Name of column in dataframe containing the conf. int. higher limits. 

logscale 
If True, make the xaxis log scale. Default is False.  
capitalize 
How to capitalize strings. Default is None. One of "capitalize", "title", "lower", "upper", "swapcase".  
form_ci_report 
If True (default), report the estimates and confidence interval beside the variable labels.  
ci_report 
If True (default), format the confidence interval as a string.  
groupvar 
Name of column in dataframe containing the variable grouping labels. 

group_order 
List of group labels indicating the order of groups to report in the plot.  
annote 
List of columns to add as annotations on the lefthand side of the plot.  
annoteheaders 
List of column headers for the lefthand side annotations.  
rightannote 
List of columns to add as annotations on the righthand side of the plot.  
right_annoteheaders 
List of column headers for the righthand side annotations.  
pval 
Name of column in dataframe containing the pvalues. 

starpval 
If True (default), format pvalues with stars indicating statistical significance.  
sort 
If True, sort variables by estimate values in ascending order. 

sortby 
Name of column to sort by. Default is estimate . 

flush 
If True (default), leftflush variable labels and annotations.  
decimal_precision 
Number of decimal places to print. (Default = 2)  
figsize 
Tuple indicating core figure size. Default is (4, 8)  
xticks 
List of xticklabels to print on xaxis.  
ylabel 
Ylabel title.  
xlabel 
Xlabel title.  
color_alt_rows 
If True, shade out alternating rows in gray.  
preprocess 
If True (default), preprocess the dataframe before plotting. 

return_df 
If True, returned the preprocessed dataframe . 
Known Issues
 Variable labels coinciding with group variables may lead to unexpected formatting issues in the graph.
 Leftflushing of annotations relies on the
monospace
font.  Plot may give strange behavior for few rows of data (six rows or fewer. see this issue)
 Plot can get cluttered with too many variables/rows (~30 onwards)
Background and Additional Resources
More about forest plots
Forest plots have many aliases (h/t Chris Alexiuk). Other names include coefplots, coefficient plots, metaanalysis plots, dotandwhisker plots, blobbograms, margins plots, regression plots, and ropeladder plots.
Forest plots in the medical and health sciences literature are plots that report results from different studies as a metaanalysis. Markers are centered on the estimated effect and horizontal lines running through each marker depicts the confidence intervals.
The simplest version of a forest plot has two columns: one for the variables/studies, and the second for the estimated coefficients and confidence intervals. This layout is similar to coefficient plots (coefplots) and is thus useful for more than metaanalyses.
More resources about forest plots
More about this package
The package is lightweight, built on pandas
, numpy
, and matplotlib
.
It is slightly opinioniated in that the aesthetics of the plot inherits some of my sensibilities about what makes a nice figure.
You can however easily override most defaults for the look of the graph. This is possible via **kwargs
in the forestplot
API (see Gallery and API options) and the matplotlib
API.
Planned enhancements include forest plots where each row can have multiple coefficients (e.g. from multiple models).
Related packages
 [1] [Stata] Jann, Ben (2014). Plotting regression coefficients and other estimates. The Stata Journal 14(4): 708737.
 [2] [Python] MetaAnalysis in statsmodels
 [3] [Python] Matt BracherSmith's Forestplot
 [4] [R] Solt, Frederick and Hu, Yue (2021) dotwhisker: DotandWhisker Plots of Regression Results
 [5] [R] Bounthavong, Mark (2021) Forest plots. RPubs by RStudio
Contributing
Contributions are welcome, and they are greatly appreciated!
Potential ways to contribute:
 Raise issues/bugs/questions
 Write tests for missing coverage
 Add features (see examples notebook for a survey of existing features)
 Add example datasets with companion graphs
 Add your graphs with companion code
Issues
Please submit bugs, questions, or issues you encounter to the GitHub Issue Tracker. For bugs, please provide a minimal reproducible example demonstrating the problem.
Pull Requests
Please feel free to open an issue on the Issue Tracker if you'd like to discuss potential contributions via PRs.
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