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Collapse heatmap #85

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bfc51a8
Python version defined.
ricoderks Oct 11, 2021
52a204d
Merge branch 'main' of github.com:ricoderks/omicser
ricoderks Oct 11, 2021
6065128
Needed to run locally
ricoderks Oct 11, 2021
7903390
Merge branch 'main' of github.com:ricoderks/omicser
ricoderks Oct 12, 2021
67ea44b
Merge remote-tracking branch 'upstream/main'
ricoderks Oct 13, 2021
01bd6d2
Merge remote-tracking branch 'upstream/main'
ricoderks Oct 14, 2021
ebaf857
checkbox for collapsing heatmap
ricoderks Oct 14, 2021
787f5a9
Collapse the heatmap.
ricoderks Oct 14, 2021
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64 changes: 48 additions & 16 deletions R/mod_pg_vis_raw.R
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,8 @@ mod_pg_vis_raw_ui <- function(id){
),
hr(style = "border-top: 1px dashed grey;"),
checkboxInput(ns("CB_scale"), "Scale values?", value = TRUE),
hr(style = "border-top: 1px dashed grey;"),
checkboxInput(ns("CB_collapse"), "Collapse heatmap?", value = FALSE),
br()

), # End of column (6 space)
Expand Down Expand Up @@ -265,22 +267,52 @@ mod_pg_vis_raw_server <- function(id, rv_data, rv_selections, heat_data){
#TODO:
# -limit levels of clustering columns
# -
ht <- ComplexHeatmap::Heatmap(in_mat,
cluster_rows = in_clust_row,
cluster_columns = in_clust_col,
column_split = grp_x,
#row_split = grp_y,
top_annotation = ha,
show_row_names = show_row_names,
right_annotation = ha2,
row_names_side = "right",
#row_names_side = "left",
row_names_gp = grid::gpar(fontsize = 7),
name = units_label,
column_title = x_title,
row_title = omics_title,
show_parent_dend_line = TRUE,
use_raster = FALSE)
if(input$CB_collapse) {
# collapse heatmap
# calculate the cluster for the rows
hc <- hclust(dist(in_mat,
method = "euclidian"),
method = "complete")

# make heatmap with empty matrix
ht <- ComplexHeatmap::Heatmap(matrix(ncol = 0,
nrow = nrow(in_mat)),
cluster_rows = hc,
# cluster_columns = in_clust_col,
# column_split = grp_x,
#row_split = grp_y,
top_annotation = ha,
show_row_names = show_row_names,
right_annotation = ha2,
row_names_side = "right",
#row_names_side = "left",
row_names_gp = grid::gpar(fontsize = 7),
name = units_label,
column_title = x_title,
row_title = omics_title,
show_parent_dend_line = TRUE,
row_dend_reorder = FALSE, # Rico: this is needed to make sure ComplexHeatmap doesn't reorder the rows after clustering
use_raster = FALSE)
} else {
# show full heatmap
ht <- ComplexHeatmap::Heatmap(in_mat,
cluster_rows = in_clust_row,
cluster_columns = in_clust_col,
column_split = grp_x,
#row_split = grp_y,
top_annotation = ha,
show_row_names = show_row_names,
right_annotation = ha2,
row_names_side = "right",
#row_names_side = "left",
row_names_gp = grid::gpar(fontsize = 7),
name = units_label,
column_title = x_title,
row_title = omics_title,
show_parent_dend_line = TRUE,
row_dend_reorder = FALSE, # Rico: this is needed to make sure ComplexHeatmap doesn't reorder the rows after clustering
use_raster = FALSE)
}

#top_annotation = HeatmapAnnotation(foo = anno_block(gp = gpar(fill = 2:4))),
#
Expand Down
4 changes: 4 additions & 0 deletions omicser.Rproj
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Expand Up @@ -19,3 +19,7 @@ BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
PackageRoxygenize: rd,collate,namespace

PythonType: conda
PythonVersion: 3.9.7
PythonPath: ~/miniconda/envs/omxr/bin/python
6 changes: 6 additions & 0 deletions omicser_options.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
database_names:
Domenico: domenico_stem_cell
Yassene: yassene_lipid
Schisto: schisto_lipids
db_root_path: /home/ricoderks/Documents/LUMC/Projects/omicser/inst/DB
conda_environment: omxr