Commit d0bd129d authored by Mathias Walzer's avatar Mathias Walzer
Browse files

adapted protein count plot code after update to ori data representation

parent 0c638511
......@@ -11,17 +11,9 @@ source("../container/postprocess/codify_study_customisations.R")
# This needs a nifty table that has all the numbers collected
protein_counts_all_projects <- read.delim("../R/protein_counts_all_projects.tsv")
pxds <- c("PXD004873", "PXD000672", "PXD004691", "PXD014943", "PXD003497", "PXD004589", "PXD014194", "PXD003539", "PXD001064", "PXD010912")
for ( i in pxds ) {
data <- get(paste("ours_",i,sep=""))(norm="median", tally=TRUE)
print(data)
}
# define order manually
PXD_order <- c("PXD004873*",
"PXD000672*",
PXD_order <- c("PXD004873",
"PXD000672",
"PXD004691",
"PXD014943",
"PXD003497",
......@@ -51,9 +43,9 @@ fdr <- ggplot(protein_counts_all_projects %>%
protein_comp <- read.delim("../R/protein_comparisons_where_available.tsv") %>%
#dplyr::rename(Reanalysis_runfiltered = Proteins..50..missing) %>%
#dplyr::rename(Original_Data = Original...data) %>%
dplyr::rename(`Original data\n (Publication)` = Original...publication) %>%
dplyr::rename(`Reanalysis\n (unfiltered)` = Total.proteins ) %>%
dplyr::rename(`Reanalysis\n (consistencyfilter)` = X.50..per.group ) %>%
dplyr::rename(`Original data\n (Publication)` = Original...after.filter) %>%
dplyr::rename(`Reanalysis\n (unfiltered)` = Reanalysis.proteins ) %>%
dplyr::rename(`Reanalysis\n (consistencyfilter)` = Reanalysis.proteins...50..per.group. ) %>%
dplyr::select(PXD,`Reanalysis\n (unfiltered)`,`Reanalysis\n (consistencyfilter)`,`Original data\n (Publication)`) %>%
tidyr::gather(Source, count, c(`Reanalysis\n (unfiltered)`,`Reanalysis\n (consistencyfilter)`,`Original data\n (Publication)`)) %>%
#mutate(count = na_if(count,"N/A")) %>%
......@@ -83,4 +75,4 @@ fdr + discovery + plot_annotation(tag_levels = 'A')
# width = 160,
# height = 106,
# units = "mm", dpi = 300
# )
\ No newline at end of file
# )
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