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Added balanced summary plot arguement
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@JTNearing-broad
JTNearing-broad committed Nov 21, 2024
1 parent 57cf479 commit 5f47739
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Showing 3 changed files with 76 additions and 16 deletions.
40 changes: 32 additions & 8 deletions R/maaslin3.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -117,6 +117,7 @@ args$max_pngs <- 30
args$cores <- 1
args$save_models <- FALSE
args$reference <- NULL
args$summary_plot_balanced <- FALSE

#### end ####

Expand Down Expand Up @@ -582,6 +583,19 @@ options <-
)
)

options <-
optparse::add_option(
options,
c("--summary_plot_balanced"),
type = "logical",
dest = "make_summary_plot_balanced",
default = args$summary_plot_balanced,
help = paste(
"If coef_plot_vars is selected this will",
"select balanced top features [ Default: %default ]"
)
)

option_not_valid_error <- function(message, valid_options) {
logging::logerror(paste(message, ": %s"), toString(valid_options))
stop("Option not valid", call. = FALSE)
Expand Down Expand Up @@ -765,7 +779,8 @@ maaslin_log_arguments <- function(input_data,
max_pngs = 30,
cores = 1,
save_models = FALSE,
verbosity = 'FINEST') {
verbosity = 'FINEST',
summary_plot_balanced=FALSE) {
# Allow for lower case variables
normalization <- toupper(normalization)
transform <- toupper(transform)
Expand Down Expand Up @@ -873,6 +888,8 @@ maaslin_log_arguments <- function(input_data,
logging::logdebug("Augment: %s", augment)
logging::logdebug("Evaluate only: %s", evaluate_only)
logging::logdebug("Cores: %d", cores)
logging::logdebug("Balanced Summary plot: %s", summary_plot_balanced)


maaslin_check_arguments(
feature_specific_covariate,
Expand Down Expand Up @@ -2307,7 +2324,8 @@ maaslin_plot_results <- function(output,
coef_plot_vars = NULL,
heatmap_vars = NULL,
plot_associations = TRUE,
max_pngs = 30) {
max_pngs = 30,
balanced=FALSE) {
# create an output folder and figures folder if it does not exist
if (!file.exists(output)) {
logging::loginfo("Creating output folder")
Expand Down Expand Up @@ -2354,7 +2372,8 @@ maaslin_plot_results <- function(output,
coef_plot_vars = coef_plot_vars,
heatmap_vars = heatmap_vars,
median_comparison_abundance = median_comparison_abundance,
median_comparison_prevalence = median_comparison_prevalence
median_comparison_prevalence = median_comparison_prevalence,
balanced=balanced
)
}

Expand Down Expand Up @@ -2416,7 +2435,8 @@ maaslin_plot_results_from_output <- function(output,
coef_plot_vars = NULL,
heatmap_vars = NULL,
plot_associations = TRUE,
max_pngs = 30) {
max_pngs = 30,
balanced=FALSE) {

# create an output folder and figures folder if it does not exist
if (!file.exists(output)) {
Expand Down Expand Up @@ -2469,7 +2489,8 @@ maaslin_plot_results_from_output <- function(output,
coef_plot_vars = coef_plot_vars,
heatmap_vars = heatmap_vars,
median_comparison_abundance = median_comparison_abundance,
median_comparison_prevalence = median_comparison_prevalence
median_comparison_prevalence = median_comparison_prevalence,
balanced=balanced
)
}

Expand Down Expand Up @@ -2602,7 +2623,8 @@ maaslin3 <- function(input_data,
max_pngs = 30,
cores = 1,
save_models = FALSE,
verbosity = 'FINEST') {
verbosity = 'FINEST',
summary_plot_balanced=FALSE) {
logging::logReset()

# Allow for lower case variables
Expand Down Expand Up @@ -2798,7 +2820,8 @@ maaslin3 <- function(input_data,
coef_plot_vars,
heatmap_vars,
plot_associations,
max_pngs
max_pngs,
balanced=summary_plot_balanced
)
},
warning = function(w) {
Expand Down Expand Up @@ -2898,6 +2921,7 @@ if (identical(environment(), globalenv()) &&
augment = current_args$augment,
evaluate_only = current_args$evaluate_only,
reference = current_args$reference,
unscaled_abundance = current_args$unscaled_abundance
unscaled_abundance = current_args$unscaled_abundance,
summary_plot_balanced=current_args$summary_plot_balanced
)
}
51 changes: 43 additions & 8 deletions R/viz.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,8 @@ make_coef_plot <- function(merged_results_sig,
max_significance,
median_comparison_prevalence,
median_comparison_abundance,
median_df) {
median_df,
plot_threshold=10) {
coef_plot_data <-
merged_results_sig[merged_results_sig$full_metadata_name %in%
coef_plot_vars,]
Expand All @@ -111,9 +112,9 @@ make_coef_plot <- function(merged_results_sig,
quantile_df <- coef_plot_data %>%
dplyr::group_by(.data$full_metadata_name) %>%
dplyr::summarise(
lower_q = median(.data$coef) - 10 *
lower_q = median(.data$coef) - plot_threshold *
(median(.data$coef) - quantile(.data$coef, 0.25)),
upper_q = median(.data$coef) + 10 *
upper_q = median(.data$coef) + plot_threshold *
(quantile(.data$coef, 0.75) - median(.data$coef))
) %>%
data.frame()
Expand Down Expand Up @@ -470,7 +471,8 @@ maaslin3_summary_plot <-
coef_plot_vars = NULL,
heatmap_vars = NULL,
median_comparison_abundance = FALSE,
median_comparison_prevalence = FALSE) {
median_comparison_prevalence = FALSE,
balanced=FALSE) {
if (first_n > 200) {
logging::logerror(
paste(
Expand Down Expand Up @@ -533,15 +535,42 @@ maaslin3_summary_plot <-

# Subset associations for plotting
merged_results_joint_only <-
unique(merged_results[, c('feature', 'qval_joint')])
unique(merged_results[, c('feature', 'qval_joint', 'full_metadata_name')])
merged_results_joint_only <-
merged_results_joint_only[
order(merged_results_joint_only$qval_joint),]
if (length(unique(merged_results_joint_only$feature)) < first_n) {
first_n <- length(unique(merged_results_joint_only$feature))
signif_taxa <-
unique(merged_results_joint_only$feature)[seq(first_n)]
}else{
#If balanced is turned on but there is not coef's choosen error out.
if(balanced){
if(is.null(coef_plot_vars)){
logging::logerror(
paste(
"Balanced plotting requires you set the variables you want to plot using
the parameter coef_plot_vars"
)
)
return()
}else{
#grab the first N feature where N=N/(length of coef_plot_var) to
#plot the coef plot
first_n_per = first_n/length(coef_plot_vars)
signif_taxa <- merged_results_joint_only %>%
dplyr::group_by(.data$full_metadata_name) %>%
dplyr::arrange(desc(-.data$qval_joint), .by_group = T) %>%
dplyr::slice_head(n=ceiling(first_n_per)) %>%
dplyr::pull(feature) %>%
unique()
}
}else{
signif_taxa <-
unique(merged_results_joint_only$feature)[seq(first_n)]
}
}
signif_taxa <-
unique(merged_results_joint_only$feature)[seq(first_n)]


merged_results_sig <- merged_results %>%
dplyr::filter(.data$feature %in% signif_taxa)
Expand Down Expand Up @@ -588,12 +617,18 @@ maaslin3_summary_plot <-
if (length(coef_plot_vars) > 0 &
sum(merged_results_sig$full_metadata_name %in%
coef_plot_vars) >= 1) {
if(balanced){
plot_thres=5
}else{
plot_thres=10
}
p1 <- make_coef_plot(merged_results_sig,
coef_plot_vars,
max_significance,
median_comparison_prevalence,
median_comparison_abundance,
median_df)
median_df,
plot_threshold = plot_thres)

} else {
p1 <- NULL
Expand Down
1 change: 1 addition & 0 deletions tests/testthat/test_maaslin_log_arguments.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,7 @@ lines_to_compare <- c("Writing function arguments to log file",
"Augment: TRUE",
"Evaluate only:",
"Cores: 9",
"Balanced Summary plot: FALSE",
"Verifying options selected are valid")

expect_starts_with <- function(strings, prefixes) {
Expand Down

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