Fig_multi_x

fig_multi_x.m creates a figure that shows one or more columns of a table plotted against another column. The formatting and arrangement of the figure is defined in a separate file provided by the user in JSON format.

Source

Parts of this document were generated using a MATLAB live script

Preliminaries 

% View an example table
single_data_file = "data/sim_prot_1_7_r1.txt";
d = readtable(data_file_string)
  time m_length m_force sc_extension sc_force hs_1_pCa hs_1_length hs_1_command_length hs_1_slack_length hs_1_a_length hs_1_m_length hs_1_force hs_1_titin_force hs_1_viscous_force hs_1_extracellular_force hs_1_inter_hs_titin_force_effect hs_1_a_pop_1 hs_1_a_pop_2 hs_1_m_pop_1 hs_1_m_pop_2 hs_1_m_pop_3 hs_1_m_pop_4 hs_1_c_pop_1 hs_1_c_pop_2 hs_1_c_pop_3
1 0.001 1100 3685.3 0.073707 3685.3 9.23 1099.9 1100 NaN 1015.9 809.12 3685.3 4420.5 -737.07 0 0 1 0 0.93499 0.065008 0 0 1 0 0
2 0.002 1100 4298 0.08596 4298 8.93 1099.9 1100 NaN 1015.9 809.12 4298 4420.2 -122.53 0 0 1 0 0.88513 0.11487 0 0 1 0 0
3 0.003 1100 4399.9 0.087997 4399.9 8.76 1099.9 1100 NaN 1015.9 809.12 4399.9 4420.2 -20.37 0 0 0.99986 0.00014468 0.8506 0.1494 0 0 1 0 0
4 0.004 1100 4416.8 0.088336 4416.8 8.64 1099.9 1100 NaN 1015.9 809.12 4416.8 4420.2 -3.3865 0 0 0.99971 0.00028935 0.82398 0.17602 0 0 1 0 0
5 0.005 1100 4419.6 0.088392 4419.6 8.54 1099.9 1100 NaN 1015.9 809.12 4419.6 4420.2 -0.56299 0 0 1 0 0.80064 0.19936 0 0 1 0 0
6 0.006 1100 4420.1 0.088401 4420.1 8.47 1099.9 1100 NaN 1015.9 809.12 4420.1 4420.2 -0.093594 0 0 0.99986 0.00014468 0.78868 0.21132 0 0 1 0 0
7 0.007 1100 4420.1 0.088403 4420.1 8.41 1099.9 1100 NaN 1015.9 809.12 4420.1 4420.2 -0.01556 0 0 0.99957 0.00043403 0.77758 0.22242 0 0 1 0 0
8 0.008 1100 4420.2 0.088403 4420.2 8.35 1099.9 1100 NaN 1015.9 809.12 4420.2 4420.2 -0.0025868 0 0 0.99957 0.00043403 0.76553 0.23447 0 0 1 0 0
9 0.009 1100 4420.2 0.088403 4420.2 8.31 1099.9 1100 NaN 1015.9 809.12 4420.2 4420.2 -0.00043258 0 0 0.99957 0.00043403 0.75309 0.24691 0 0 1 0 0
10 0.01 1100 4420.2 0.088403 4420.2 8.26 1099.9 1100 NaN 1015.9 809.12 4420.2 4420.2 -6.9858e-05 0 0 0.99899 0.0010127 0.74817 0.25183 0 0 1 0 0
11 0.011 1100 4420.2 0.088403 4420.2 8.23 1099.9 1100 NaN 1015.9 809.12 4420.2 4420.2 -1.1305e-05 0 0 0.99913 0.00086806 0.74093 0.25907 0 0 1 0 0
12 0.012 1100 4420.2 0.088403 4420.2 8.19 1099.9 1100 NaN 1015.9 809.12 4420.2 4420.2 -1.9008e-06 0 0 0.99913 0.00086806 0.73708 0.26292 0 0 1 0 0
13 0.013 1100 4420.2 0.088403 4420.2 8.16 1099.9 1100 NaN 1015.9 809.12 4420.2 4420.2 -3.8426e-07 0 0 0.99913 0.00086806 0.73293 0.26707 0 0 1 0 0
14 0.014 1100 4420.2 0.088403 4420.2 8.14 1099.9 1100 NaN 1015.9 809.12 4420.2 4420.2 -1.0232e-07 0 0 0.99884 0.0011574 0.73052 0.26948 0 0 1 0 0 
% View a simple template
template_file_1 = "templates/template_1.json";
t = readstruct(template_file_1)

t = struct with fields:
        layout: [1x1 struct]
     x_display: [1x1 struct]
    formatting: [1x1 struct]
        panels: [1x1 struct]

Link to the template file

{
    "layout":
    {
        "fig_width": 3.5,
        "padding_left": 1,
        "padding_right": 1,
        "padding_top": [0.2, 0.05],
        "padding_bottom": [0.05, 0.5],
        "x_to_y_ratio": 2
    },
    "x_display":{
        "global_x_field": "time",
        "label": "Time (s)"
    },
    "formatting":
    {
        "label_font_size": 9,
        "x_axis_offset": 0.1,
        "x_label_offset": -0.45,
        "x_tick_length": 0.1,
        "x_tick_label_vertical_offset": -0.12,
        "y_axis_offset": 0.2,
        "y_label_offset": -0.5,
        "y_tick_length": 0.1,
        "y_tick_label_horizontal_offset": -0.16,
        "tick_font_size": 9,
        "legend_font_size": 7,
        "legend_alignment": "top_left",
        "legend_position": [1.2, 1.0]        
    },
    "panels":
    [
        {
            "column": 1,
            "y_info":
            {
                "label": "Stress\n(kN^{-2})",
                "series":
                [
                    
                    {
                        "field": "m_force"
                    }
                ]
            }
        }
    ]
}

Simplest figure 

% Create a figure
figure_multi_x(single_data_file, template_file_1)

Figure

Plot data from multiple files 

% Plot three tables with the same format
multiple_data_files = [ ...
    "data/sim_prot_1_1_r1.txt", ...
    "data/sim_prot_1_3_r1.txt", ...
    "data/sim_prot_1_5_r1.txt"];

figure_multi_x(multiple_data_files, template_file_1)

Figure

Plot multiple panels

Add new panels to the figure by inserting new elements into the panel array. The column variable defines where the panel will be placed.

template_file_2 = "templates/template_2.json";

figure_multi_x(single_data_file, template_file_2)

Link to the template file

{
    <SNIP>

    "panels":
    [
        {
            "column": 1,
            "y_info":
            {
                "label": "Stress\n(kN^{-2})",
                "series":
                [
                    {
                        "field": "m_force"
                    }
                ]
            }
        },
        {
            "column": 2,
            "y_info":
            {
                "label": "Half-\nsarcomere\nlength\n(nm)",
                "series":
                [                    
                    {
                        "field": "hs_1_length"
                    }
                ]
            }
        }
    ]
}

Figure

Plot multiple rows

Add another panel to column 2 by inserting a new element with the appropriate column label. Only the bottom panel in each column shows the x axis.

template_file_3 = "templates/template_3.json";

figure_multi_x(single_data_file, template_file_3)

{
    <SNIP>

    "panels":
    [
        {
            "column": 1,
            "y_info":
            {
                "label": "Stress\n(kN^{-2})",
                "series":
                [
                    {
                        "field": "m_force"
                    }
                ]
            }
        },
        {
            "column": 2,
            "y_info":
            {
                "label": "Half-\nsarcomere\nlength\n(nm)",
                "series":
                [                    
                    {
                        "field": "hs_1_length"
                    }
                ]
            }
        },
        {
            "column": 2,
            "y_info":
            {
                "label": "Actin\npopulations",
                "series":
                [
                    
                    {
                        "field": "hs_1_a_pop_1"
                    }
                ]
            }
        }
    ]
}

Figure

Plot multiple traces from the same data file

Each panel can show more than one trace. If a field_label is provided, a legend will be added to the panel.

template_file_4 = "templates/template_4.json";

figure_multi_x(single_data_file, template_file_4)

{

    <snip>

    "panels":
    [
        <snip>
         {
            "column": 2,
            "y_info":
            {
                "label": "Actin\npopulations",
                "series":
                [
                    
                    {
                        "field": "hs_1_a_pop_1",
                        "field_label": "State 1"
                    },
                    {
                        "field": "hs_1_a_pop_2",
                        "field_label": "State 2"
                    }
                ]
            }
        }
    ]
}

Figure

Putting it all together

With this:

figure_multi_x(data_file, template_file)

generates

Figure