#' @title lipaallmacro_fishertest
#'
#' @description (LipaTg)Tests for Lipa in macrophages populations in GFP+/GFP-.
#'
#' @param output Output of lipa_expressionmarkers
#' @param counts Output of originalcount
#' @param alt "two.sided", "greater", "less"
#'
#' @return A dataframe of the fisher's test output for Lipa in macrophage
#' subpopulations of GFP+/GFP-.
#'
#' @examples lipa.40pc_0.2 <- lipaallmacro_fishertest(plaque.combined_40pc_0.2,
#' counts = counts_40pc_0.2, alt = "two.sided")
#'
#'
#'
#' @export
#' @importFrom dplyr "%>%"
#'
lipaallmacro_fishertest <- function(output, counts, alt = "two.sided"){
Lipa_prop = left_join(output, counts) %>%
mutate(
GFPneg.n_lipa = round(GFPnegative.pct*GFPnegative),
GFPpos.n_lipa = round(GFPpositive.pct*GFPpositive)) %>%
dplyr::select(cluster, GFPpos.n_lipa, GFPneg.n_lipa, GFPpositive, GFPnegative,
GFPnegative.pct, GFPpositive.pct, p_val, p_val_adj, clusterlabels)
Lipa_prop <- Lipa_prop[grep("macrophages", Lipa_prop$clusterlabels),]
sums <- colSums(Lipa_prop[,2:5])
a_1 <- rbind(sums[1], sums[3]-sums[1])
a_2 <- rbind(sums[2], sums[4]-sums[2])
a <- cbind(a_1,a_2)
rownames(a) <- c("Lipa", "no_Lipa")
colnames(a) <- c("GFPPos", "GFPNeg")
return(unlist(fisher.test(a, alternative=alt)[1:3]))
}
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