Commit f30e47a5 authored by peguerin's avatar peguerin
Browse files

permutation figure S5 S6

parent 139d97fa
......@@ -275,7 +275,7 @@ Rscript 00-scripts/step5/supplementary_figures/figureS4.R
#### 4.5.4.5 Taxonomic coverage of the sequences used by the model
* input : [watertype_all_modeles_effectives_family.csv](11-sequences_taxonomy_habitat/watertype_all_modeles_effectives_family.csv)
* output : [figureS6.pdf](10-figures/figureS5.pdf)
* output : [figureS5.pdf](10-figures/figureS5.pdf)
```
Rscript 00-scripts/step5/supplementary_figures/figureS5.R
```
......@@ -283,7 +283,7 @@ Rscript 00-scripts/step5/supplementary_figures/figureS5.R
#### 4.5.4.6 Sampling effect
* inputs : [total_data_genetic_diversity_with_all_descripteurs.tsv](09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv), [grid_equalarea200km](01-infos/grid_equalarea200km), [ne_50m_rivers_lake_centerlines_scale_rank](01-infos/ne_50m_rivers_lake_centerlines_scale_rank), [GSHHS_h_L2.shp](01-infos/big_lakes/GSHHS_h_L2.shp)
* output : [figureS5.tiff](10-figures/figureS6.tiff)
* output : [figureS6.tiff](10-figures/figureS6.tiff)
```
Rscript 00-scripts/step5/supplementary_figures/figureS6.R
```
......
......@@ -173,7 +173,14 @@ Scripts are classified by step (see [Table of contents](#-table-of-contents)) an
- output :
* [figureS4.pdf](10-figures/figureS3.pdf)
* [figureS5.R](00-scripts/step5/supplementary_figures/figureS5.R) : it generates maps of the number of species by cell, number of sequences by cell and number of sequences by species by cell.
* [figureS5.R](00-scripts/step5/supplementary_figures/figureS6.R) : barplot of sequences number and species number by taxonomic family/order
- input :
* [watertype_all_modeles_effectives_family.csv](11-sequences_taxonomy_habitat/watertype_all_modeles_effectives_family.csv)
- output :
* [figureS5.pdf](10-figures/figureS5.pdf)
* [figureS6.R](00-scripts/step5/supplementary_figures/figureS5.R) : it generates maps of the number of species by cell, number of sequences by cell and number of sequences by species by cell.
- inputs :
* [total_data_genetic_diversity_with_all_descripteurs.tsv](09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv)
* [grid_equalarea200km](01-infos/grid_equalarea200km)
......@@ -181,13 +188,8 @@ Scripts are classified by step (see [Table of contents](#-table-of-contents)) an
* [ne_50m_rivers_lake_centerlines_scale_rank](01-infos/ne_50m_rivers_lake_centerlines_scale_rank)
* [GSHHS_h_L2.shp](01-infos/big_lakes/GSHHS_h_L2.shp)
- output :
* [figureS5.tiff](10-figures/figureS5.tiff)
* [figureS6.tiff](10-figures/figureS6.tiff)
* [figureS6.R](00-scripts/step5/supplementary_figures/figureS6.R) : barplot of sequences number and species number by taxonomic family/order
- input :
* [watertype_all_modeles_effectives_family.csv](11-sequences_taxonomy_habitat/watertype_all_modeles_effectives_family.csv)
- output :
* [figureS6.pdf](10-figures/figureS6.pdf)
* [figureS7.R](00-scripts/step5/supplementary_figures/figureS7.R) : it generates maps of the taxonomic coverage by cells for _marine_ and _freshwater_ species
- inputs :
......
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