Inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test. Outputs RRHO results, hypermatrix heatmap, rank rank scatter, metric scatter.
Usage
run_RRHO(
sig1,
sig2,
sig1_name,
sig2_name,
sig1_low = NA,
sig1_high = NA,
sig2_low = NA,
sig2_high = NA,
key = "gene",
metric1 = "sign_log_p",
metric2 = metric1,
steps = NULL,
savename = NULL,
webtool = TRUE,
BY = FALSE,
hm_method = c("ggplot", "lattice"),
palette = "Spectral",
waterfall = TRUE,
scatter = TRUE,
plot_fmt = "png"
)Arguments
- sig1
string/dataframe; path or df for sig1, with cols
keyandmetric1- sig2
string/dataframe; path or df for sig2, with cols
keyandmetric2- sig1_name
string; description of sig1
- sig2_name
string; description of sig2
- sig1_low
string; description of low sig1 values
- sig1_high
string; description of high sig1 values
- sig2_low
string; description of low sig2 values
- sig2_high
string; description of high sig2 values
- key
string; colname of corresponding values btwn both sigs
- metric1
string; colname of sig1 metric to rank by
- metric2
string; colname of sig2 metric to rank by
- steps
integer; RRHO step size
- savename
string; filepath to save results under (no extension)
- webtool
logical; T to output text formatted for Graeber RRHO webtool
- BY
logical; T for Benjamini-Yekutieli FDR corrected pvalues
- hm_method
string; make heatmap with ggplot geom_raster or lattice levelplot
- palette
string; RColorBrewer continuous palette name
- waterfall
logical;
TRUEto include waterfall subplots (hm_method = "ggplot"only)- scatter
logical;
TRUEto output metric & rank scatterplot- plot_fmt
string; file extension to save plot as