PFOCR Stats

This R notebooks prepares counts and figures to summarize PFOCR activity. The output files are displayed on the website and used in publications and grant applications.

Read PFOCR .rds files

Set the path to these files

Read in files

figs <- readRDS(file.path(local.path,"pfocr_figures_draft.rds"))
genes <- readRDS(file.path(local.path,"pfocr_genes_draft.rds"))
chems <- readRDS(file.path(local.path,"pfocr_chemicals_draft.rds"))
dis <- readRDS(file.path(local.path,"pfocr_diseases_draft.rds"))

Contents and counts

papers <- figs %>%
    distinct(pmcid)
papers_hs <- figs %>%
    dplyr::filter(grepl('Homo sapiens',organisms_ner)) %>%
    distinct(pmcid)
figures_hs <- figs %>%
    dplyr::filter(grepl('Homo sapiens',organisms_ner)) %>%
    distinct(figid)
ncbigenes <- genes %>%
    distinct(ncbigene_id)
ncbigenes_hs <- genes %>%
    dplyr::filter(organism_id == 9606) %>%
    distinct(ncbigene_id)
chemicals_mesh <- chems %>%
    distinct(mesh)
chemicals_chebi <- chems %>%
    distinct(chebi)
diseases_mesh <- dis %>%
    distinct(mesh)
diseases_doid <- dis %>%
    distinct(doid)
fig.num <- nrow(figs)
paper.num <- nrow(papers)
fig.hs.num <- nrow(figures_hs)
paper.hs.num <- nrow(papers_hs)
gene.total <- nrow(genes)
gene.unique <- paste(nrow(ncbigenes), "(ncbigene)")
gene.hs.unique <- paste(nrow(ncbigenes_hs), "(human)")
chem.total <- nrow(chems)
chem.unique.mesh <- paste(nrow(chemicals_mesh), "(mesh)")
chem.unique.chebi <- paste(nrow(chemicals_chebi), "(chebi)")
di.total <- nrow(dis)
di.unique.mesh <- paste(nrow(diseases_mesh), "(mesh)")
di.unique.doid <- paste(nrow(diseases_doid), "(doid)")

data <- data.frame(Total = c(gene.total,chem.total,di.total), Unique = c(gene.unique, chem.unique.mesh, di.unique.mesh), Specific = c(gene.hs.unique, chem.unique.chebi, di.unique.doid))
row.names(data) = c("Genes", "Chemicals", "Diseases")

The Pathway Figure OCR project has identified 110408 pathway figures from 93057 published papers.

  Total Unique Specific
Genes 4,687,583 147974 (ncbigene) 18586 (human)
Chemicals 346,094 14212 (mesh) 6785 (chebi)
Diseases 44,598 1632 (mesh) 673 (doid)

Contents extracted from figures

Main page plot

years.plot <- figs %>%
    dplyr::filter(!is.na(year)) %>%
      group_by(year) %>%
      dplyr::summarize(fig_cnt = n())

min.year = min(years.plot$year)
max.year = max(years.plot$year)
    
p <- years.plot %>%
      ggplot(aes(x=factor(year, levels = seq(min.year, max.year)), y=fig_cnt, 
                 fill = case_when(
                   year == max.year ~ "no",
                   year < max.year ~ "yes"
                 ))) +
      geom_bar(stat="identity") +
      ggtitle("Published Pathway Figures by Year") +
      xlab("") + 
      ylab("") +
      scale_x_discrete(breaks = factor(seq(min.year,max.year,by=5)), drop=FALSE)  +
      scale_fill_manual(values = c("yes" = "#3955E7", "no" = "#7995F7" ), guide = "none" ) + 
      theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 4),
            axis.text.y = element_text(size = 5),
            text = element_text(size = 4, ,  family="Helvetica", face="plain"),
            panel.grid.major = element_line(color="#eeeeee"), 
            plot.title = element_text(hjust = 0.5,vjust = -15),
          panel.background = element_rect(fill='transparent'), #transparent panel bg
          plot.background = element_rect(fill='transparent', color=NA), #transparent plot bg
          panel.grid.minor = element_blank(), #remove minor gridlines
          legend.background = element_rect(fill='transparent'), #transparent legend bg
          legend.box.background = element_rect(fill='transparent') #transparent legend panel
      ) 

p


ggsave("../assets/img/pfocr_stats.png", plot = last_plot(), 
       width = 1100, height = 600, units = "px", dpi = 450, bg='transparent')

Counts