Skip to content

add group counts and proportions to output of summary functions #36

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
clabornd wants to merge 1 commit into
base: master
Choose a base branch
from
Open

add group counts and proportions to output of summary functions #36

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion R/summarizeGroupComparisons.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,8 @@ getGroupComparisonSummaryFunctionNames <- function() {
})

new_fdata <- do.call(rbind, lapply(edata_cols, function(x) attr(x, "f_data")))
new_edata <- data.frame(compData$e_data[, getEDataColName(compData)], do.call(cbind, edata_cols))
new_fdata$Comparison_Summary_Column <- make.unique(new_fdata$Comparison_Summary_Column)
new_edata <- data.frame(setNames(compData$e_data[, getEDataColName(compData)], getEDataColName(compData)), do.call(cbind, edata_cols))
colnames(new_edata)[1] <- getEDataColName(compData)

if (inherits(compData, "peakData")) {
Expand Down
19 changes: 17 additions & 2 deletions R/uniqueness_functions.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,13 @@ uniqueness_nsamps <- function(edata_df, group_df, data_scale, pres_thresh, absn_
res_vec[which(numpres$N_grp1 <= absn_thresh & numpres$N_grp2 >= pres_thresh)] = paste("Unique to", grps[2], sep = " ")

lvls <- c(paste("Unique to", grps), "Observed in Both")
data.frame(uniqueness_nsamps = factor(res_vec, levels = lvls))
out_df = data.frame(uniqueness_nsamps = factor(res_vec, levels = lvls))
out_df = dplyr::bind_cols(
out_df,
numpres
)

return(out_df)
}


Expand Down Expand Up @@ -161,7 +167,16 @@ uniqueness_prop <- function(edata_df, group_df, data_scale, pres_thresh, absn_th
res_vec[which(prop_pres$prop_grp1 <= absn_thresh & prop_pres$prop_grp2 >= pres_thresh)] = paste("Unique to", grps[2], sep = " ")

lvls <- c(paste("Unique to", grps), "Observed in Both")
data.frame(uniqueness_prop = factor(res_vec, levels=lvls))
out_df = data.frame(
uniqueness_prop = factor(res_vec, levels=lvls)
)

out_df = dplyr::bind_cols(
out_df,
prop_pres
)

return(out_df)
}


Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test_summarizeComparisons.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -70,13 +70,13 @@ test_that("test of summarizeGroupComparisons with multiple summary functions on

expect_true(inherits(grpCompSummary, "comparisonSummary"))
expect_false(inherits(grpCompSummary, "groupComparison"))
expect_equal(ncol(grpCompSummary$e_data), 7)
expect_equal(ncol(grpCompSummary$e_data), 11)
expect_true(getEDataColName(grpComp) %in% colnames(grpCompSummary$e_data))
expect_true(all(dim(grpComp$e_meta) == dim(grpCompSummary$e_meta)))
expect_true(all(colnames(grpComp$e_meta) %in% colnames(grpCompSummary$e_meta)))
expect_true(all(c("uniqueness_gtest", "uniqueness_nsamps", "uniqueness_prop") %in%
grpCompSummary$f_data$Summary_Function_Name))
expect_equal(nrow(grpCompSummary$f_data), 6)
expect_equal(nrow(grpCompSummary$f_data), 10)
expect_true(all(unlist(lapply(grpCompSummary$e_data[, 2], function(x) is.factor(x)))))

})
Loading