PlotPlants

Set global font

The PyPlot package of Julia uses sans font by default, by my favorite font is serif type. Also, some fonts do not have normal greek letters in their library, like the Times only have italic greek letters. To change the default font to serif and use normal greek letters, the PlotPlants package provides a use_serif_tex function, which use LaTeX amsmath and upgreek packages. Also, sans-serif font and normal text render are also supported.

PlotPlants.use_sans — Function

use_sans()

Set default font to sans-serif

PlotPlants.use_sans_tex — Function

use_sans_tex()

Set default font to sans and use latex wrapper for texts

PlotPlants.use_sans_text — Function

use_sans_text()

Set default font to sans and use normal text wrapper for texts

PlotPlants.use_serif — Function

use_serif()

Set default font to serif

PlotPlants.use_serif_tex — Function

use_serif_tex()

Set default font to serif and use latex wrapper for texts

PlotPlants.use_serif_text — Function

use_serif_text()

Set default font to serif and use normal text wrapper for texts

Symbols and units

To facilitate the use of LaTeX packages, functions latex_symbol and latex_unit are provided to rapidly generate equation symbols and units. By default,

if the number of letters is one, the letter will be set to italic, otherwise, the letters will be normal (not italic);
if the letter is greek, the letter will be normal;
all sub- and super-scripts are normal;

PlotPlants.latex_symbol — Function

latex_symbol(
            mid::String;
            sub::String = "",
            sup::String = "",
            presub::String = "",
            presup::String = "",
            option::String = "mathrm"
)

Return the latex symbol string, given

mid Center symbol, italic only when length>1
sub Optional: subscript after the mid
sup Optional: supscript after the mid
presub Optional: subscript before the mid
presup Optional: supscript before the mid
option Optional: choose from text and mathrm (default)

PlotPlants.latex_unit — Function

latex_unit(id::String;
           paren::Bool = true,
           squared::Bool = false,
           space::Bool = true,
           unicode::Bool = false
)

Return the unit, given

id Identifier of the unit (if not in libary, use id as unit)
paren Optional: if true, include parenthesis
squared Optional: if true, use [], otherwise, use ()
space Optional: if true, add a SPACE at the beginning
unicode Optional. If true, return unicode; otherwise, return upgreek string

The predefined units include

A μmol CO₂ m⁻² s⁻¹
E mol H₂O m⁻² s⁻¹
E_MMOL mmol H₂O m⁻² s⁻¹
G mol m⁻² s⁻¹
PAR μmol m⁻² s⁻¹
T °C
WUE μmol mol⁻¹

PlotPlants.parse_symbol — Function

parse_symbol(letter::String, unicode::Bool=false)

Return the unicode or latex string, given

id Identifier for the greek letter, e.g., "alpha"
unicode Optional. If true, return unicode; otherwise, return upgreek string

PlotPlants.subscript — Function

subscript(ss::Number; option="mathrm", standalone=true)
subscript(ss::String; option="mathrm", standalone=true)

Return a string of subscript, given

PlotPlants.superscript — Function

superscript(ss::Number; option="mathrm", standalone=true)
superscript(ss::String; option="mathrm", standalone=true)

Return a string of superscript, given

Create and save canvas

An customized funtion create_canvas is provided to genrate figure and an array of axis from a few keywords. For example,

create_canvas(fig_id) returns a figure with one axis;
create_canvas(fig_id, nrow=2, ncol=2) returns a figure will four subplots;
create_canvas(fig_id, nrow=2, ncol=2, axs=[1,2,4]) returns a figure with three subplot (the left bottom panel is empty);

PlotPlants.create_canvas — Function

create_canvas(
            id::Union{Int,String};
            ncol::Int = 1,
            nrow::Int = 1,
            axids::Array{Int,1} = Int[],
            figsize::Tuple{Number,Number} = (0.5+ncol*3, 0.5+nrow*3),
            dpi::Number = 100
)

Create a canvas, given

id ID of the figure
ncol Number of columns in the figure
nrow Number of rows in the figure
axids Given indicies of the subplots in the figure
figsize Given canvas size
dpi Given pixels per inch

PlotPlants.save_canvas! — Function

save_canvas!(fig::Figure, path::String, saving::Bool = false)

Save a canvas, given

fig Canvas to save
path Path to save the figure
saving Optional. If true, save the figure

PlotPlants.save_gif! — Function

save_gif!(figs::Array, fps::Int, gif::String)
save_gif!(imgs::Array{Array,1}, fps::Int, fn::String)

Save an array of figures as GIF, given

figs An array of figures
fps Frame per second
fn File name of the GIF to save
imgs An array of array (loaded figures)

Shapes

A few customized shapes can be added to the canvas very conveniently, for example, stoma and ellipse. These shortcut functions include

PlotPlants.plot_ellipse! — Function

plot_ellipse!(
            ax::PyObject,
            xy::Tuple{Number,Number};
            width::Number = 10,
            height::Number = 10,
            angle::Number = 0,
            color::String = "black",
            edgecolor::String = color,
            facecolor::String = color,
            alpha::Number = 0.5
)

Plot an ellipse on axis, given

ax Axis to plot on
xy Center of the ellipse
width Width of the ellipse
height Height of the ellipse
angle Rotation angle of the ellipse
color Color of the ellipse
edgecolor Edgecolor of the ellipse
facecolor Face color of the ellipse
alpha Transparency of the ellipse

PlotPlants.plot_stoma! — Function

plot_stoma!(
           ax::PyObject,
           xy::Tuple{Number,Number};
           width::Number = 10,
           height::Number = 10,
           stoma::Number = 0.2,
           angle::Number = 0
)

Plot a stoma on the axis, given

ax Axis to plot on
xy Center of the stoma
width Width of the stoma
height Height of the stoma
stoma Stomatal pore width ratio
angle Rotation angle of the stoma

Set titles, lims, ticks, and ticklabels

Function set_titles! will add panel titles like (a) to all the panels, and if labels options is given, the labels will be added after the letter (e.g., (a) label).

PlotPlants.set_titles! — Function

set_titles!(axs::Array;
            labels::Array{String,1} = String[],
            paren::Bool = true,
            capital::Bool = false,
            dotsep::Bool = false,
            fontsize::Number = 16,
            loc::String = "center",
            usetex::Bool = true
)

Set titles for the axes, given

axs An array of axis
labels Optional: labels after the panel title, e.g., (a) label
paren Optional: if true, use format like (a)
capital Optional: if true, use capital letters like (A)
dotsep Optional: if true, add a dot after the label like (a).
fontsize Optional: fontsize of the title
loc Optional: location of the title
usetex Optional: use latex render

Similarly, the package provides shortcuts to set the X-axis and Y-axis labels, limits, ticks, and tick labels.

PlotPlants.set_xlabels! — Function

set_xlabels!(
            axs::Array,
            xlabels::Array{String,1};
            fontsize::Number = 16
)
set_xlabels!(
            axs::Array,
            xlabels::String;
            fontsize::Number = 16
)

Set X-axis labels for the axes, given

axs An array of axis
labels X-axis labels
fontsize Optional: fontsize of the label

PlotPlants.set_ylabels! — Function

set_ylabels!(
            axs::Array,
            ylabels::Array{String,1};
            fontsize::Number = 16
)
set_ylabels!(
            axs::Array,
            ylabels::String;
            fontsize::Number = 16
)

Set Y-axis labels for the axes, given

axs An array of axis
labels Y-axis labels
fontsize Optional: fontsize of the label

PlotPlants.set_xylabels! — Function

set_xylabels!(
            axs::Array,
            xlabels::Union{Array{String,1},String},
            ylabels::Union{Array{String,1},String};
            fontsize::Number = 16
)

Set X-axis and Y-axis labels for the axes, given

axs An array of axis
xlabels X-axis labels
ylabels Y-axis labels
fontsize Optional: fontsize of the label

PlotPlants.set_xlims! — Function

set_xlims!(axs::Array, xlims::Array)
set_xlims!(axs::Array,
           xlims::Union{Array{Int,1},Array{Float32,1},Array{Float64,1}}
)

Set the X-axis limits, given

axs Array of axis
xlims Array of X-axis limits

PlotPlants.set_ylims! — Function

set_ylims!(axs::Array, ylims::Array)
set_ylims!(axs::Array,
           ylims::Union{Array{Int,1},Array{Float32,1},Array{Float64,1}}
)

Set the Y-axis limits, given

axs Array of axis
ylims Array of Y-axis limits

PlotPlants.set_xylims! — Function

set_xylims!(axs::Array, xlims::Array, ylims::Array)

Set the X-axis limits, given

axs Array of axis
xlims Array of X-axis limits
ylims Array of Y-axis limits

PlotPlants.set_xticks! — Function

set_xticks!(axs::Array, xticks::Array)
set_xticks!(axs::Array,
            xticks::Union{Array{Int,1},Array{Float32,1},Array{Float64,1}}
)

Set X-axis ticks for a given

axs Array of axis
xticks Array of X-axis ticks

PlotPlants.set_yticks! — Function

set_yticks!(axs::Array, yticks::Array)
set_yticks!(axs::Array,
            yticks::Union{Array{Int,1},Array{Float32,1},Array{Float64,1}}
)

Set Y-axis ticks for a given

axs Array of axis
yticks Array of Y-axis ticks

PlotPlants.set_xyticks! — Function

set_xyticks!(axs::Array, xticks::Array, yticks::Array)

Set Y-axis ticks for a given

axs Array of axis
xticks Array of X-axis ticks
yticks Array of Y-axis ticks

PlotPlants.set_xticklabels! — Function

set_xticklabels!(axs::Array, xticklabs::Array)
set_xticklabels!(axs::Array, xticklabs::Array{String,1})

Set X-axis ticks for a given

axs Array of axis
xticklabs Array of X-axis tick labels

PlotPlants.set_yticklabels! — Function

set_yticklabels!(axs::Array, yticklabs::Array)
set_yticklabels!(axs::Array, yticklabs::Array{String,1})

Set Y-axis ticks for a given

axs Array of axis
yticklabs Array of Y-axis tick labels

PlotPlants.set_xyticklabels! — Function

set_xyticklabels!(axs::Array, xticklabs::Array, yticklabs::Array)

Set X-axis and Y-axis ticks for a given

axs Array of axis
xticklabs Array of X-axis tick labels
yticklabs Array of Y-axis tick labels

Add regression

To quickly plot the regression lines, users may use

PlotPlants.plot_line_regress! — Function

plot_line_regress!(
            ax::PyObject,
            xs::Array,
            ys::Array;
            linestyle::String = "-",
            intercept::Bool = true,
            interval::Bool = false,
            color::String = "red",
            alpha::Number = 0.3
)

Plor linear regression and confidence interval on the axis, given

ax Given axis
xs Array of x
ys Array of y
linestyle Optional. Line style for the regression curve ("-" by default)
intercept Optional: if true, fit the data with an intercept
interval Optional: if true, plot the confidence interval of fitted y
color Color the fitted curve
alpha Transparency of the confidence interval (same color as curve)

The function will filter out the NaN from the given data, make linear regression using function line_regress, sort the results by the value of x from low to high, store the results in a LinearRegressionResult type struct, and plot the regression line on the given axis. Also, if interval is set to true, the function will also plot the confidence intervals of the predicted y.

PlotPlants.linear_df_xy — Function

linear_df_xy(df::DataFrame, intercept::Bool)

Linear fit the X and Y in a given DataFrame, given

df DataFrame that use X and Y to store values
intercept Whether using intercept when making the regression

PlotPlants.line_regress — Function

line_regress(
            xs::Array,
            ys::Array;
            intercept::Bool = true,
            sorting::Bool = true
)

Make linear regression and return the fitted results, given

xs Array of x, can be NaN
ys Array of y, can be NaN
intercept Optional: if true use intercept in the fitting
sorting Optional: if true, sort the values

PlotPlants.LinearRegressionResult — Type

mutable struct LinearRegressionResult

Fields

lm::Any
Regression result
r2::Number
Adjusted R square
inter::Number
Intercept of fitting
slope::Number
Slope of fitting
inter_p::Number
P value of intercept
slope_p::Number
P value of slopes
inter_ci::Array
Confidence interval of intercept
slope_ci::Array
Confidence interval of slopes
df::DataFrames.DataFrame
Predictions DataFrame

Further, the PlotPlants module provides a quick tool to test whether the slope differs from a given value, see

PlotPlants.test_slope — Function

test_slope(xs::Array,
           ys::Array;
           slope::Number = 0,
           intercept::Bool = true
)

Make linear regression and return the p value of whether the regression slope differs from the given slope, given

xs Array of x, can be NaN
ys Array of y, can be NaN
slope Slope to test
intercept Optional: if true use intercept in the fitting

Density plot

PlotPlants.calculate_density — Function

calculate_density(xs::Array, ys::Array)
calculate_density(xs::Array, ys::Array, nthread::Int)

Plot density plot on axis, given

xs Array of X
ys Array of Y
nthread Number of threads to run in parallel

PlotPlants.plot_density! — Function

plot_density!(
            ax::PyObject,
            xs::Array,
            ys::Array;
            cmap::String = "viridis",
            markersize::Number = 8,
            dmax::Number = NaN
)
plot_density!(
            ax::PyObject,
            df::DataFrame;
            cmap::String = "viridis",
            markersize::Number = 8,
            dmax::Number = NaN
)

Plot density plot on axis, given

ax Axis to plot on
xs Array of X
ys Array of Y
cmap Optional. Color map scheme
markersize Optional. Marker size dimension, scatter size is markersize^2
dmax Maximal density. If dmax is not NaN, use dmax as maximum density
df A dataframe with column names of ("X","Y","C")

PlotPlants.plot_hexbin! — Function

plot_hexbin!(
            ax::PyObject,
            xs::Array,
            ys::Array;
            cmap::String = "Greys",
            logbins::Bool = false,
            gridsize::Number = 25
)
plot_hexbin!(
            ax::PyObject,
            xs::Array,
            ys::Array,
            xlims::Array,
            ylims::Array;
            cmap::String = "Greys",
            logbins::Bool = false,
            gridsize::Number = 25
)

Plot density plot on axis, given

ax Axis to plot on
xs Array of X
ys Array of Y
cmap Optional. Color map scheme
logbins Optional. If true, use log(count) to color the bins
gridsize Number of bins on both directions
xlim Limits of x axis. Used to make plot region equal among subplots
ylim Limits of y axis. Used to make plot region equal among subplots

Preview dataset

PlotPlants.preview_data — Function

preview_data(
            xs::Array,
            ys::Array;
            title = randstring(10),
            figsize::Tuple{Number,Number} = (4,3),
            xlab::String = "X label",
            ylab::String = "Y label",
            marker::String = "",
            linestyle::String = "-",
            label_fontsize::Int = 12
)

Preview data, given

xs Array of x
ys Array of y
title Axis titile
figsize Canvas size
xlab X axis label
ylab Y axis label
marker Marker style
linestyle Line style
label_fontsize X and Y axes label font size

PlotPlants.preview_dataset! — Function

preview_dataset!(ax::PyObject, filename::String, label)
preview_dataset!(
            ax::PyObject,
            filename::String,
            label::String,
            format::FormatNC
)

Preview dataset, given

filename Dataset file to preview
label Label of the data to preview, variable name in NC files, band name in TIFF files
format AbstractFormat type file format

PlotPlants.AbstractFormat — Type

abstract type AbstractFormat

Hierachy of AbstractFormat

FormatTIFF
FormatNC

PlotPlants.FormatNC — Type

struct FormatNC

PlotPlants.FormatTIFF — Type

struct FormatTIFF