Skip to content

Commit

Permalink
addExtraParamsToPlt range 0 was changed to 0.2
Browse files Browse the repository at this point in the history
  • Loading branch information
barizona committed Sep 13, 2024
1 parent 3c222a1 commit d6b2dde
Show file tree
Hide file tree
Showing 5 changed files with 23 additions and 34 deletions.
14 changes: 7 additions & 7 deletions R/Plotting.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -207,7 +207,7 @@ reshape_results <- function(model = NULL, model_results = NULL,
#' p_value_type_colname = "eFDR")

plot_graph <- function(reshaped_results, ontology_id_colname='ontology_id',
ontology_element_colname='element_id_in_ontology',
ontology_element_colname = 'element_id_in_ontology',
shared_elements_min_threshold = 0,
p_value_type_colname = 'eFDR', p_value_max_threshold = 0.05) {
ontology_id <- ontology_id_colname
Expand Down Expand Up @@ -242,9 +242,9 @@ plot_graph <- function(reshaped_results, ontology_id_colname='ontology_id',
edges)))) {
graph_plot <- graph_plot +
ggraph::geom_edge_arc(aes(width = .data$weight), alpha = 0.5)}
graph_plot <- addExtraParamsToPlt(graph_plot=graph_plot,
p_value_max_threshold=p_value_max_threshold,
p_value_type_colname=p_value_type_colname)
graph_plot <- addExtraParamsToPlt(graph_plot = graph_plot,
p_value_max_threshold = p_value_max_threshold,
p_value_type_colname = p_value_type_colname)
graph_plot
}

Expand Down Expand Up @@ -294,13 +294,13 @@ fillOntologiesGrapgEdge <- function(ontologies, ontology_id,
addExtraParamsToPlt <- function(graph_plot, p_value_max_threshold,
p_value_type_colname) {graph_plot <- graph_plot +
ggraph::scale_edge_width(breaks = scales::pretty_breaks(n = 5),
range = c(0, 3), name="Nr. of shared elements") +
range = c(0.2, 3), name = "Nr. of shared elements") +
ggraph::geom_node_point(aes(color = .data$p_stat)) +
ggraph::geom_node_point(aes(color = .data$p_stat,
size = (1 - .data$p_stat)), show.legend = FALSE) +
scale_size_area(max_size = 10) +
scale_color_gradient2(mid = '#ff6361', high = 'grey90',
limits = c(0.0,p_value_max_threshold),
limits = c(0.0, p_value_max_threshold),
name = p_value_type_colname) +
ggraph::geom_node_text(aes(label = .data$label), repel = TRUE) +
ggraph::theme_graph(base_family = "sans")
Expand Down Expand Up @@ -405,7 +405,7 @@ plot_barplot <- function(reshaped_results, ontology_id_colname = 'ontology_id',
fill = p_value_type_colname)) +
geom_bar(stat = "identity") +
scale_fill_gradient2(mid = '#ff6361', high = 'grey90',
limits = c(0.0,p_value_max_threshold),
limits = c(0.0, p_value_max_threshold),
name = p_value_type_colname) +
coord_flip() +
theme_light()
Expand Down
10 changes: 2 additions & 8 deletions README.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -349,10 +349,7 @@ plot_graph(reshaped_results = ora_reshaped_results,
# Upper threshold for the value indicating the significance
p_value_max_threshold = 0.05,
# Column that indicates the significance values
p_value_type_colname = "eFDR") +
# Scaling the edge width
ggraph::scale_edge_width_continuous(range = c(0.2, 3),
breaks = c(2, 4, 6, 8, 10))
p_value_type_colname = "eFDR")
```

**Visualising the Associations: Heatmap**
Expand Down Expand Up @@ -543,10 +540,7 @@ plot_graph(reshaped_results = gsea_reshaped_results,
# upper threshold for the value indicating the significance
p_value_max_threshold = 0.05,
# column that indicates the significance values
p_value_type_colname = "adjusted_p_value") +
# Scaling the edge width
ggraph::scale_edge_width_continuous(range = c(0.2, 3),
breaks = c(20, 40, 60, 80))
p_value_type_colname = "adjusted_p_value")
```

Other plot types such as lollipop plots, bar plots, and heatmaps can also be used to investigate the GSEA results.
Expand Down
33 changes: 14 additions & 19 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -478,10 +478,7 @@ plot_graph(reshaped_results = ora_reshaped_results,
# Upper threshold for the value indicating the significance
p_value_max_threshold = 0.05,
# Column that indicates the significance values
p_value_type_colname = "eFDR") +
# Scaling the edge width
ggraph::scale_edge_width_continuous(range = c(0.2, 3),
breaks = c(2, 4, 6, 8, 10))
p_value_type_colname = "eFDR")
```

<img src="man/figures/README-network_plot_ora-1.png" width="60%" />
Expand Down Expand Up @@ -693,7 +690,7 @@ gsea_results %>%
filter(adjusted_p_value < 0.05) %>%
# the number of such rows
nrow()
#> [1] 8
#> [1] 9
```

Inspect the significant results:
Expand All @@ -708,14 +705,15 @@ gsea_results %>%

| ontology_id | ontology_name | nr_common_with_tested_elements | p_value | adjusted_p_value |
|:------------|:--------------|-------------------------------:|----------:|-----------------:|
| LexA | LexA | 53 | 0.0000000 | 0.0000037 |
| FNR | FNR | 259 | 0.0000784 | 0.0059976 |
| ArcA | ArcA | 148 | 0.0002848 | 0.0087152 |
| GlaR | GlaR | 3 | 0.0002484 | 0.0087152 |
| ModE | ModE | 45 | 0.0002666 | 0.0087152 |
| SoxS | SoxS | 37 | 0.0006182 | 0.0157647 |
| DnaA | DnaA | 13 | 0.0007556 | 0.0165154 |
| PaaX | PaaX | 14 | 0.0014082 | 0.0269323 |
| LexA | LexA | 53 | 0.0000001 | 0.0000089 |
| FNR | FNR | 259 | 0.0000379 | 0.0028982 |
| GlaR | GlaR | 3 | 0.0002188 | 0.0111583 |
| ArcA | ArcA | 148 | 0.0003258 | 0.0117944 |
| DnaA | DnaA | 13 | 0.0004397 | 0.0117944 |
| ModE | ModE | 45 | 0.0004625 | 0.0117944 |
| SoxS | SoxS | 37 | 0.0007464 | 0.0163152 |
| PspF | PspF | 7 | 0.0016107 | 0.0308049 |
| PaaX | PaaX | 14 | 0.0019054 | 0.0323922 |

### Visualising the GSEA Results

Expand Down Expand Up @@ -747,10 +745,7 @@ plot_graph(reshaped_results = gsea_reshaped_results,
# upper threshold for the value indicating the significance
p_value_max_threshold = 0.05,
# column that indicates the significance values
p_value_type_colname = "adjusted_p_value") +
# Scaling the edge width
ggraph::scale_edge_width_continuous(range = c(0.2, 3),
breaks = c(20, 40, 60, 80))
p_value_type_colname = "adjusted_p_value")
```

<img src="man/figures/README-network_plot_gsea-1.png" width="60%" />
Expand Down Expand Up @@ -949,7 +944,7 @@ ordered_set %>%
sessionInfo()
#> R version 4.4.1 (2024-06-14)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.4 LTS
#> Running under: Ubuntu 22.04.5 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
Expand All @@ -976,7 +971,7 @@ sessionInfo()
#>
#> loaded via a namespace (and not attached):
#> [1] fastmatch_1.1-4 gtable_0.3.5 xfun_0.47
#> [4] ggrepel_0.9.5 lattice_0.22-6 tzdb_0.4.0
#> [4] ggrepel_0.9.6 lattice_0.22-6 tzdb_0.4.0
#> [7] vctrs_0.6.5 tools_4.4.1 generics_0.1.3
#> [10] curl_5.2.2 parallel_4.4.1 fansi_1.0.6
#> [13] highr_0.11 pkgconfig_2.0.3 Matrix_1.7-0
Expand Down
Binary file modified man/figures/README-network_plot_gsea-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified man/figures/README-network_plot_ora-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.

0 comments on commit d6b2dde

Please sign in to comment.