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1 # Flux to Map
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2
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3 Visualize flux distributions on metabolic pathway maps.
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4
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5 ## Overview
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6
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7 This tool analyzes and visualizes statistical differences in reaction fluxes of groups of samples, returned by the Flux Simulation tool. The results can be visualized on s SVG metabolic map.
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8
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9 ## Galaxy Interface
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10
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11 In Galaxy: **COBRAxy → Metabolic Flux Enrichment Analysis**
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12
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13 1. Upload flux data and sample class file
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14 2. Select the map and configure the comparison type
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15 3. Click **Run tool**
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16
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17 ## Command-line console
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18
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19 ```bash
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20 flux_to_map -input_data fluxes.csv \
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21 -input_class classes.csv \
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22 -choice_map ENGRO2 \
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23 -comparison manyvsmany \
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24 -pvalue 0.05 \
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25 -idop output/
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26 ```
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27
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28 ## Parameters
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29
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30 | Parameter | Flag | Description | Default |
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31 |-----------|------|-------------|---------|
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32 | Input Data | `-input_data` | Flux data file | - |
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33 | Input Class | `-input_class` | Sample class definitions | - |
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34 | Map Choice | `-choice_map` | ENGRO2, Recon, or Custom | ENGRO2 |
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35 | Custom Map | `-custom_map` | Path to custom SVG map | - |
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36 | Comparison | `-comparison` | manyvsmany, onevsrest, onevsmany | manyvsmany |
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37 | P-value | `-pvalue` | Significance threshold | 0.05 |
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38 | FDR Correction | `-fdr` | Apply FDR correction | true |
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39 | Test Type | `-test_type` | t, wilcoxon, ks | t |
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40 | Color Map | `--color_map` | Color scheme: viridis or jet | viridis |
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41 | Output Path | `-idop` | Output directory | flux_to_map/ |
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42
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43 ## Input Formats
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44
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45 ### Flux Data
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46
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47 ```
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48 Reaction Sample1 Sample2 Sample3
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49 R00001 12.5 8.5 14.2
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50 R00002 -6.5 13.5 7.2
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51 ```
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52
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53 ### Sample Classes
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54
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55 ```
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56 SampleID Class
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57 Sample1 Control
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58 Sample2 Treatment
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59 Sample3 Treatment
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60 ```
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61
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62 **Note on Metabolic Map**
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63 We provide a default SVG map for the ENGRO2 model. If another model is used, we suggest uploading a custom SVG map.
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64
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65 **File Format Notes:**
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66 - Use **tab-separated** values (TSV) or **comma-separated** (CSV)
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67 - First row must contain column headers
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68 - Sample names must match between flux data and class file
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69 - Class names should not contain spaces
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70
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71 ## Statistical Tests
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72
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73 - **t**: Student's t-test (parametric, assumes normality)
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74 - **wilcoxon**: Wilcoxon/Mann-Whitney (non-parametric)
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75 - **ks**: Kolmogorov-Smirnov (distribution-free)
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76
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77 ## Comparison Types
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78
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79 - **manyvsmany**: All pairwise class comparisons
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80 - **onevsrest**: Each class vs all others
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81 - **onevsmany**: One reference vs multiple classes
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82
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83 ## Output
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84
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85 - `*_map.svg`: Annotated pathway maps
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86 - `comparison_results.tsv`: Statistical results
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87 - `*.log`: Processing log
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88
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89 ## Examples
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90
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91 ### Basic Comparison
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92
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93 ```bash
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94 flux_to_map -input_data fluxes.csv \
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95 -input_class classes.csv \
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96 -choice_map ENGRO2 \
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97 -comparison manyvsmany \
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98 -pvalue 0.05 \
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99 -idop results/
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100 ```
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101
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102 ### With Custom Map
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103
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104 ```bash
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105 flux_to_map -input_data fluxes.csv \
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106 -input_class classes.csv \
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107 -choice_map Custom \
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108 -custom_map pathway.svg \
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109 -comparison onevsrest \
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110 -test_type wilcoxon \
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111 -idop results/
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112 ```
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113
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114 ## Troubleshooting
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115
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116 | Error | Solution |
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117 |-------|----------|
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118 | "No matching reactions" | Verify reaction ID consistency |
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119 | "Insufficient data" | Increase sample sizes |
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120
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121 ## See Also
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122
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123 - [MAREA](tools/marea)
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124 - [Flux Simulation](tools/flux-simulation)
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125 - [Built-in Models](reference/built-in-models)
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