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bug fix and minor improvements #86

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merged 8 commits into from
Jan 23, 2025
Merged

bug fix and minor improvements #86

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12733a0
now showTumorSampleBarcode works in stacked mode
rdmorin Jan 9, 2025
ea62a10
Merge branch 'rmorin-dev' of github.com:morinlab/GAMBLR.viz into rmor…
rdmorin Jan 9, 2025
bd4e5c4
add some flexiblity and new colour option
rdmorin Jan 12, 2025
a21e859
Merge branch 'rmorin-dev' of github.com:morinlab/GAMBLR.viz into rmor…
rdmorin Jan 13, 2025
be9b79c
document
rdmorin Jan 13, 2025
56c48a7
Merge branch 'rmorin-dev' of github.com:morinlab/GAMBLR.viz into rmor…
rdmorin Jan 13, 2025
b45abfb
update documentation
rdmorin Jan 13, 2025
7069e50
cleanup: documentation
Kdreval Jan 23, 2025
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41 changes: 31 additions & 10 deletions R/prettyOncoplot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -273,7 +273,12 @@ prettyOncoplot = function(
Hugo_Symbol,
Variant_Classification = value
)

maf_df_noncoding <- inner_join(maf_df, nc)
if(verbose){
print(nc)
print(maf_df_noncoding)
}
} else {
# Make empty maf_df
maf_df_noncoding <- maf_df %>%
Expand Down Expand Up @@ -1126,7 +1131,7 @@ prettyOncoplot = function(
cluster_rows=T,
cluster_cols=F,
fontsize_row = 6,
show_colnames = F
show_colnames = showTumorSampleBarcode
)
if(verbose){
print("Done!")
Expand All @@ -1139,7 +1144,7 @@ prettyOncoplot = function(
cluster_cols=T,
cluster_rows=F,
fontsize_row = 6,
show_colnames = F
show_colnames = showTumorSampleBarcode
)
}else{
message("clustering mutation rows and columns")
Expand All @@ -1148,7 +1153,7 @@ prettyOncoplot = function(
clustering_distance_rows=clustering_distance_rows,
clustering_distance_cols=clustering_distance_cols,
fontsize_row = 6,
show_colnames = F)
show_colnames = showTumorSampleBarcode)
}
if(dry_run){
print(h_obj)
Expand Down Expand Up @@ -1423,7 +1428,7 @@ make_prettyoncoplot = function(mat_input,
message("re-clustering columns based on numeric metadata")

hh = Heatmap(heat_mat,cluster_columns=T,
clustering_distance_columns = clustering_distance_cols)
clustering_distance_columns = clustering_distance_cols,show_column_names = showTumorSampleBarcode)
col_order = NULL
col_dend = column_dend(hh)

Expand All @@ -1441,6 +1446,9 @@ make_prettyoncoplot = function(mat_input,
if(verbose){
print(oncoprint_args)
}
if(showTumorSampleBarcode){
heatmap_args[['show_column_names']] = TRUE
}
if(numeric_heatmap_location == "top"){
if(!missing(splitColumnName)){
heatmap_args[['column_split']] = column_split
Expand All @@ -1450,11 +1458,17 @@ make_prettyoncoplot = function(mat_input,
}
if(verbose){
print(names(heatmap_args))

print(names(oncoprint_args))
print(oncoprint_args)
}
if(return_inputs){
oncoprint_heatmap = do.call("oncoPrint",oncoprint_args)
numeric_heatmap = do.call("Heatmap",heatmap_args)
}
ht_list =
do.call("Heatmap",heatmap_args) %v%
do.call("oncoPrint",oncoprint_args) %v%

ComplexHeatmap::HeatmapAnnotation(df = metadata_df_numeric,
show_legend = show_legend,
col = colours,
Expand All @@ -1465,19 +1479,25 @@ make_prettyoncoplot = function(mat_input,
col_fun = col_fun,
ncol = 1,
direction = legend_direction,
labels_gp = gpar(fontsize = legendFontSize)))
labels_gp = gpar(fontsize = legendFontSize))) %v%
do.call("oncoPrint",oncoprint_args)



draw(ht_list)
if(return_inputs){
return(list(Heatmap=ht_list,heat_mat=heat_mat,mut_mat=mat_input))
return(list(Oncoprint=oncoprint_heatmap,Numeric=numeric_heatmap,Full_Heatmap=ht_list,heat_mat=heat_mat,mut_mat=mat_input))
}
return()
}else if(numeric_heatmap_location == "bottom"){
if(return_inputs){
oncoprint_heatmap = do.call("oncoPrint",oncoprint_args)
numeric_heatmap = do.call("Heatmap",heatmap_args)
}

ht_list =
do.call("oncoPrint",oncoprint_args) %v%
do.call("Heatmap",heatmap_args) %v%

ComplexHeatmap::HeatmapAnnotation(df = metadata_df_numeric,
show_legend = show_legend,
col = colours,
Expand All @@ -1488,13 +1508,14 @@ make_prettyoncoplot = function(mat_input,
col_fun = col_fun,
ncol = 1,
direction = legend_direction,
labels_gp = gpar(fontsize = legendFontSize)))
labels_gp = gpar(fontsize = legendFontSize))) %v%
do.call("Heatmap",heatmap_args)



draw(ht_list)
if(return_inputs){
return(list(Heatmap=ht_list,heat_mat=heat_mat,mut_mat=mat_input))
return(list(Oncoprint=oncoprint_heatmap,Numeric=numeric_heatmap,Full_Heatmap=ht_list,heat_mat=heat_mat,mut_mat=mat_input))
}
return()
}
Expand Down
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