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chore: plot params NA -> NULL
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@jiajic
jiajic committed May 1, 2024
1 parent 26b5b3a commit 4cfbe1c
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Showing 44 changed files with 211 additions and 211 deletions.
8 changes: 4 additions & 4 deletions R/auxiliary_giotto.R
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Original file line number Diff line number Diff line change
Expand Up @@ -115,9 +115,9 @@ filterDistributions <- function(gobject,
fill_color = 'lightblue',
scale_axis = 'identity',
axis_offset = 0,
show_plot = NA,
return_plot = NA,
save_plot = NA,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = 'filterDistributions') {

Expand Down Expand Up @@ -281,7 +281,7 @@ filterCombinations <- function(gobject,
y_axis_offset = 0,
show_plot = TRUE,
return_plot = FALSE,
save_plot = NA,
save_plot = NULL,
save_param = list(),
default_save_name = 'filterCombinations') {

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6 changes: 3 additions & 3 deletions R/clustering.R
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Original file line number Diff line number Diff line change
Expand Up @@ -379,9 +379,9 @@ doGiottoClustree <- function(gobject,
res_vector = NULL,
res_seq = NULL,
return_gobject = FALSE,
show_plot = NA,
save_plot = NA,
return_plot = NA,
show_plot = NULL,
save_plot = NULL,
return_plot = NULL,
save_param = list(),
default_save_name = "clustree",
verbose = TRUE,
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2 changes: 1 addition & 1 deletion R/cross_section.R
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Original file line number Diff line number Diff line change
Expand Up @@ -882,7 +882,7 @@ insertCrossSectionGenePlot3D <- function(
show_other_cells = F,
axis_scale = c("cube", "real", "custom"),
custom_ratio = NULL,
show_plot = NA, return_plot = NA, save_plot = NA,
show_plot = NULL, return_plot = NULL, save_plot = NULL,
save_param = list(),
default_save_name = "spatGenePlot3D_with_cross_section",
...
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18 changes: 9 additions & 9 deletions R/dimension_reduction.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1262,9 +1262,9 @@ screePlot = function(gobject,
ncp = 100,
ylim = c(0, 20),
verbose = TRUE,
show_plot = NA,
return_plot = NA,
save_plot = NA,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = 'screePlot',
...) {
Expand Down Expand Up @@ -1486,9 +1486,9 @@ jackstrawPlot = function(gobject,
iter = 10,
threshold = 0.01,
verbose = TRUE,
show_plot = NA,
return_plot = NA,
save_plot = NA,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = 'jackstrawPlot') {

Expand Down Expand Up @@ -1656,9 +1656,9 @@ signPCA <- function(gobject,
jack_threshold = 0.01,
jack_ylim = c(0, 1),
verbose = TRUE,
show_plot = NA,
return_plot = NA,
save_plot = NA,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = 'signPCA') {

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12 changes: 6 additions & 6 deletions R/spatial_enrichment_visuals.R
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Original file line number Diff line number Diff line change
Expand Up @@ -102,9 +102,9 @@ plotCellTypesFromEnrichment <- function(gobject = NULL,
title = NULL,
save_param = list(),
default_save_name = 'cell_types_from_enrichment',
save_plot = NA,
show_plot = NA,
return_plot = NA){
save_plot = NULL,
show_plot = NULL,
return_plot = NULL){
# guard clauses handled at first step downstream
# therefore, omitting here.
id_and_types = findCellTypesFromEnrichment(gobject = gobject,
Expand Down Expand Up @@ -165,9 +165,9 @@ pieCellTypesFromEnrichment <- function(gobject = NULL,
title = NULL,
save_param = list(),
default_save_name = 'cell_types_from_enrichment_pie',
save_plot = NA,
show_plot = NA,
return_plot = NA){
save_plot = NULL,
show_plot = NULL,
return_plot = NULL){
# guard clauses handled one step downstream

freq_table = findCellTypesFromEnrichment(gobject = gobject,
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34 changes: 17 additions & 17 deletions R/spatial_genes.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1976,9 +1976,9 @@ spatialDE <- function(gobject = NULL,
sig_alpha = 0.5,
unsig_alpha = 0.5,
python_path = NULL,
show_plot = NA,
return_plot = NA,
save_plot = NA,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = 'SpatialDE'){

Expand Down Expand Up @@ -2675,9 +2675,9 @@ showPattern2D <- function(gobject,
grid_border_color = 'grey',
show_legend = T,
point_size = 1,
show_plot = NA,
return_plot = NA,
save_plot = NA,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = 'showPattern2D') {

Expand Down Expand Up @@ -2786,9 +2786,9 @@ showPattern3D <- function(gobject,
x_ticks = NULL,
y_ticks = NULL,
z_ticks = NULL,
show_plot = NA,
return_plot = NA,
save_plot = NA,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = 'showPattern3D') {

Expand Down Expand Up @@ -2884,9 +2884,9 @@ showPatternGenes <- function(gobject,
top_neg_genes = 5,
point_size = 1,
return_DT = FALSE,
show_plot = NA,
return_plot = NA,
save_plot = NA,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = 'showPatternGenes') {

Expand Down Expand Up @@ -3800,9 +3800,9 @@ heatmSpatialCorFeats = function(gobject,
show_column_dend = F,
show_row_names = F,
show_column_names = F,
show_plot = NA,
return_plot = NA,
save_plot = NA,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = 'heatmSpatialCorFeats',
...) {
Expand Down Expand Up @@ -3916,9 +3916,9 @@ heatmSpatialCorGenes = function(...) {
rankSpatialCorGroups = function(gobject,
spatCorObject,
use_clus_name = NULL,
show_plot = NA,
show_plot = NULL,
return_plot = FALSE,
save_plot = NA,
save_plot = NULL,
save_param = list(),
default_save_name = 'rankSpatialCorGroups') {

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12 changes: 6 additions & 6 deletions R/spatial_interaction_spot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1203,9 +1203,9 @@ plotICFSpot <- function(gobject,
source_markers,
ICF_features,
cell_color_code = NULL,
show_plot = NA,
return_plot = NA,
save_plot = NA,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = 'plotICFSpot') {

Expand Down Expand Up @@ -1301,9 +1301,9 @@ plotCellProximityFeatSpot = function(gobject,
zscores_column = c('cell_type', 'features'),
direction = c('both', 'up', 'down'),
cell_color_code = NULL,
show_plot = NA,
return_plot = NA,
save_plot = NA,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = 'plotCellProximityFeats') {

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