diff --git a/f-generate_mean_sd_plot.R b/f-generate_mean_sd_plot.R index 1e41fead..5aafcd33 100644 --- a/f-generate_mean_sd_plot.R +++ b/f-generate_mean_sd_plot.R @@ -11,18 +11,19 @@ col_spec <- cols( antiviral <- c("Gemcitabine", "Trametinib", "Withaferin A", "Saracatinib", "Erlotinib", "Alvocidib", "Itrazole", "Elesclomol", - "Dasatinib", "Panobinostat") + "Dasatinib", "Panobinostat", "Parthenolide", "Lapatinib", + "Sorafenib", "Auranofin", "Selumetinib") trial <- c("Gallocatechin Gallate", "Genistein", "Imatinib", "Dexamethasone Acetate", "Simvastatin", "Sirolimus", "Tamoxifen") -key <- c("Gemcitabine", "Trametinib", "Withaferin A", "Saracatinib") +key <- c("Gemcitabine", "Trametinib", "Withaferin A", "Saracatinib", "Selumetinib", "Auranofin") data <- read_csv("results/ace2-summarized-dataset.csv", col_types = col_spec) %>% mutate( - class = if_else((avg >= 0.5 & sdev <= 0.06), "novel", "filtered"), + class = if_else((avg >= 0.47 & sdev <= 0.08), "novel", "filtered"), class = if_else(compound %in% antiviral, "antiviral", class), class = if_else(compound %in% trial, "trial", class), class = if_else(compound %in% key, "key", class), @@ -46,8 +47,8 @@ g <- ggplot(data, aes(x = avg, y = sdev, group = class, color = class, shape = c p <- g + geom_point(size = 5) + scale_x_continuous(breaks = seq(0.32, 0.7, 0.02), limits = c(0.4, 0.7)) + scale_y_reverse(breaks = seq(0, 0.15, 0.01), limits = c(0.10, 0)) + - geom_vline(xintercept = 0.5, color = "darkred", lwd = 1.5) + - geom_hline(yintercept = 0.06, color = "darkred", lwd = 1.5) + + geom_vline(xintercept = 0.47, color = "darkred", lwd = 1.5) + + geom_hline(yintercept = 0.08, color = "darkred", lwd = 1.5) + scale_color_manual(breaks = c("key", "antiviral", "trial", "novel", "filtered"), labels = c("Key Recommendations", "Known Anti-viral Properties", diff --git a/f-generate_upset_figure.R b/f-generate_upset_figure.R index b60335ae..95f14974 100644 --- a/f-generate_upset_figure.R +++ b/f-generate_upset_figure.R @@ -9,10 +9,10 @@ col_spec <- cols( slog2 = col_double() ) -sars2 <- read_csv("results/sars2-summarized-dataset.csv", col_types = col_spec) %>% +sars2 <- read_csv("results/ace2-summarized-dataset.csv", col_types = col_spec) %>% pull(compound) -sars2_fda <- read_csv("results/sars2-summarized-dataset.csv", col_types = col_spec) %>% +sars2_fda <- read_csv("results/ace2-summarized-dataset.csv", col_types = col_spec) %>% filter(str_detect(compound, "CHEMBL", negate = T), str_detect(compound, "SCHEMBL", negate = T), str_detect(compound, "^\\d+", negate = T), @@ -71,9 +71,9 @@ dataset_unfiltered <- list(sars2 = sars2, covidc = covidc, covidm = covidm) -dataset_fda <- list(`SARS-CoV2` = sars2_fda, - `China` = covidc_fda, - `Mt. Sinai` = covidm_fda) +dataset_fda <- list(`GSE147507 CL` = sars2_fda, + `GSE145926` = covidc_fda, + `GSE147507 PS` = covidm_fda) #upset(fromList(dataset_all), nsets = length(dataset_all)) #upset(fromList(dataset_unfiltered), nsets = length(dataset_unfiltered)) diff --git a/figures/SARS2-Mean-SD-Plot.jpg b/figures/SARS2-Mean-SD-Plot.jpg index 9e05091f..b175cd12 100644 Binary files a/figures/SARS2-Mean-SD-Plot.jpg and b/figures/SARS2-Mean-SD-Plot.jpg differ diff --git a/figures/SARS2-Mean-SD-Plot.pdf b/figures/SARS2-Mean-SD-Plot.pdf index 4f62e3f1..9b68dfa6 100644 Binary files a/figures/SARS2-Mean-SD-Plot.pdf and b/figures/SARS2-Mean-SD-Plot.pdf differ diff --git a/figures/SARS2-Mean-SD-Plot.png b/figures/SARS2-Mean-SD-Plot.png index 641f63c6..3fc86bdd 100644 Binary files a/figures/SARS2-Mean-SD-Plot.png and b/figures/SARS2-Mean-SD-Plot.png differ diff --git a/figures/sars2-china-mtsinai_comparison_upset.jpeg b/figures/sars2-china-mtsinai_comparison_upset.jpeg index 42d0fbb8..ceb923be 100644 Binary files a/figures/sars2-china-mtsinai_comparison_upset.jpeg and b/figures/sars2-china-mtsinai_comparison_upset.jpeg differ diff --git a/figures/sars2-china-mtsinai_comparison_upset.pdf b/figures/sars2-china-mtsinai_comparison_upset.pdf index 3aac375d..a2b6a4ea 100644 Binary files a/figures/sars2-china-mtsinai_comparison_upset.pdf and b/figures/sars2-china-mtsinai_comparison_upset.pdf differ diff --git a/figures/sars2-china-mtsinai_comparison_upset.png b/figures/sars2-china-mtsinai_comparison_upset.png index 77a24874..1b1dfb6f 100644 Binary files a/figures/sars2-china-mtsinai_comparison_upset.png and b/figures/sars2-china-mtsinai_comparison_upset.png differ