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Giotto v4.0.4
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- `createGiottoVisiumObject()` now generates `giottoLargeImages` instead of `giottoImage`. The `largeImage_name` param will need to be used in plotting functions for Visium following this update. Tutorials will also need to be updated to use this param in order to have the images show up.
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jiajic authored Feb 29, 2024
2 parents d66bc01 + b2cbb98 commit 7c6471c
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2 changes: 2 additions & 0 deletions .Rbuildignore
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^README\.Rmd$
^CODE_OF_CONDUCT\.md$
^INDEX.md$
^CNAME$

^docs
^vignettes
^\.github
^testdata

^codecov\.yml$
^_pkgdown\.yml$
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20 changes: 11 additions & 9 deletions .github/workflows/covr.yml
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Expand Up @@ -23,7 +23,7 @@ jobs:
steps:

- name: Checkout repo for workflow access
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Set up R environment
uses: r-lib/actions/setup-r@v2
Expand All @@ -37,16 +37,18 @@ jobs:
_R_CHECK_RD_XREFS: false
with:
dependencies: '"hard"' # do not use suggested dependencies
extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::covr
install-pandoc: false
extra-packages: |
any::rcmdcheck
any::testthat
any::rlang
any::R.utils
any::covr
any::remotes
any::hdf5r
github::drieslab/GiottoData
needs: coverage

- name: Set up dependencies (GiottoData)
run: |
suppressWarnings({
remotes::install_github('drieslab/GiottoData', build = FALSE)
})
shell: Rscript {0}

- name: Generate coverage report
run: |
covr::codecov(
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2 changes: 1 addition & 1 deletion .github/workflows/lintr.yml
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Expand Up @@ -33,7 +33,7 @@ jobs:

steps:
- name: Checkout code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Set up R environment
uses: r-lib/actions/setup-r@v2
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16 changes: 14 additions & 2 deletions .github/workflows/main_check.yaml
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Expand Up @@ -42,7 +42,7 @@ jobs:
shell: bash

- name: Checkout repo for workflow access
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Set up R environment
uses: r-lib/actions/setup-r@v2
Expand All @@ -58,13 +58,25 @@ jobs:
_R_CHECK_RD_XREFS: false
with:
dependencies: '"hard"' # do not use suggested dependencies
extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::covr, any::spdep, any::future.apply, github::drieslab/GiottoData
install-pandoc: false
extra-packages: |
any::rcmdcheck
any::testthat
any::hdf5r
any::rlang
any::R.utils
any::remotes
any::spdep
any::future.apply
github::drieslab/GiottoData
- name: Test python env install
run: |
if (!GiottoClass::checkGiottoEnvironment()) {
GiottoClass::installGiottoEnvironment()
}
reticulate::py_list_packages(envname = "giotto_env")
shell: Rscript {0}

- name: Run R CMD check
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53 changes: 0 additions & 53 deletions .github/workflows/pkgdown.yaml

This file was deleted.

6 changes: 3 additions & 3 deletions DESCRIPTION
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@@ -1,6 +1,6 @@
Package: Giotto
Title: Spatial Single-Cell Transcriptomics Toolbox
Version: 4.0.3
Version: 4.0.4
Authors@R: c(
person("Ruben", "Dries", email = "[email protected]",
role = c("aut", "cre")),
Expand Down Expand Up @@ -32,7 +32,7 @@ Depends:
utils (>= 3.5.0),
R (>= 3.5.0),
methods,
GiottoClass (>= 0.1.1)
GiottoClass (>= 0.2.0)
Imports:
BiocParallel,
BiocSingular,
Expand All @@ -42,7 +42,7 @@ Imports:
dbscan (>= 1.1-3),
ggplot2 (>= 3.1.1),
ggrepel,
GiottoUtils (>= 0.1.1),
GiottoUtils (>= 0.1.6),
GiottoVisuals (>= 0.1.1),
igraph (>= 1.2.4.1),
jsonlite,
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49 changes: 38 additions & 11 deletions NEWS.md
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@@ -1,20 +1,47 @@

# Giotto 4.0.4

## Breaking changes
* Remove `do_manual_adj` and image adjustment params from `createGiottoVisiumObject()`
* `createGiottoVisiumObject()` now creates `giottoLargeImage` for spatial images.
* `exprCellCellcom()` deprecated `gene_set_*` params removed

## Bug fixes
* Fix metadata appending/sorting issues introduced by *GiottoClass v0.1.3* (2024/01/12). Affected functions: `addHMRF()`, `addFeatsPerc()`, `doScrubletDetect()`
* `findNetworkNeighbors()` now has default `spatial_network_name` value of `NULL`
* `get10Xmatrix()` now obeys `split_by_type = FALSE`

## Changes
* Deprecate `set.seed` in favor of `seed` param for `binSpect()`
* `binSpect()` now sets a seed by default for reproducibility
* pkgdown files moved to separate [repo](https://github.com/drieslab/Giotto_website)

## Enhancements
* Use `mixedsort()` for unique clusters metadata info
* Remove unnecessary matrix densification and expose `seed` param in `doScrubletDetect()`
* Remove unnecessary matrix densification in `makeSignMatrixRank()`


# Giotto 4.0.3 (2024/02/20)


## Bug fixes
- Remove old argument `type_default = list(pal = c('blue', 'yellow', 'red'))` in plotRankSpatvsExpr()
* Remove old argument `type_default = list(pal = c('blue', 'yellow', 'red'))` in plotRankSpatvsExpr()


# Giotto 4.0.2 (2023/12/21)

## Bug Fixes
- fix bug in `doHclust()`
* fix bug in `doHclust()`

## Changes
* Move *GiottoClass* back to depends to fix access to some generics


# Giotto 4.0.1 (2023/12/16)

## Breaking Changes
* Remove `cell_ids` param for `calculateHVF` in favor of simpler `random_subset`
## Breaking changes
* Remove `cell_ids` param for `calculateHVF()` in favor of simpler `random_subset`
* Move *GiottoUtils*, *GiottoClass*, and *GiottoVisuals* to imports

## Added
Expand All @@ -32,7 +59,7 @@

# Giotto 4.0.0 (2023/11/29)

## Breaking Changes
## Breaking changes
* Update to modular package organization with the main packages being `GiottoUtils`, `GiottoClass`, `GiottoVisuals`, and `Giotto` as the analytical umbrella package.

## Added
Expand All @@ -55,7 +82,7 @@

# Giotto 3.3.1 (2023/08/02)

## Breaking Changes
## Breaking changes

* Change `checkGiottoEnvironment()`. Downgrade from error to message and return FALSE when a provided directory does not exist

Expand Down Expand Up @@ -110,7 +137,7 @@

# Giotto 3.3.0 (2023/04/18)

## Breaking Changes
## Breaking changes

* Set Suite as default branch
* Removed all deprecated accessors from `accessors.R`
Expand Down Expand Up @@ -168,7 +195,7 @@

# Giotto 3.2.0 (2023/02/02)

## Breaking Changes
## Breaking changes

* Removed support for deprecated nesting in `@nn_network` slot
* `createSpatialNetwork()` will now output a `spatialNetworkObj` by default when `return_gobject = FALSE`. It is possible to change this back to the data.table output by setting `output = 'data.table'`
Expand Down Expand Up @@ -254,7 +281,7 @@

# Giotto 3.0.0 (2022/11/18)

## Breaking Changes
## Breaking changes

* S4 subobjects framework will require giotto objects to be remade

Expand All @@ -279,7 +306,7 @@

# Giotto 2.1.0 (2022/11/09)

## Breaking Changes
## Breaking changes

* Update of python version to **3.10.2** [details](https://giottosuite.readthedocs.io/en/latest/additionalinformation.html#giotto*suite*2*1*0*2202*11*09)

Expand Down Expand Up @@ -316,7 +343,7 @@
* Deprecate `combineInteractionChangedGenes()`, `combineICG()`, `combineCPG()` in favor of `combineInteractionChangedFeats()` and `combineICF()`
* Deprecate `combineCellProximityGenes_per_interaction()` in favor of `combineCellProximityFeatures_per_interaction()`

## Breaking Changes
## Breaking changes

* ICF output internal object structure names have changed to use feats instead of genes

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10 changes: 5 additions & 5 deletions R/auxiliary_giotto.R
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Expand Up @@ -1306,7 +1306,7 @@ addFeatStatistics <- function(gobject,
feat_type = feat_type,
spat_unit = spat_unit,
new_metadata = feat_stats,
by_column = T,
by_column = TRUE,
column_feat_ID = 'feats')

## update parameters used ##
Expand Down Expand Up @@ -1581,15 +1581,15 @@ addFeatsPerc = function(gobject,

totalsum = colSums_flex(expr_data)
feat_sum = colSums_flex(expr_data[rownames(expr_data) %in% feats,])
perc_feats = round((feat_sum/totalsum)*100, 2)
perc_feats = round((feat_sum/totalsum) * 100, 2)

if(return_gobject == TRUE) {
if(return_gobject) {
temp_gobj = addCellMetadata(gobject = gobject,
spat_unit = spat_unit,
feat_type = feat_type,
new_metadata = perc_feats,
vector_name = vector_name,
by_column = F)
by_column = TRUE)

## update parameters used ##
temp_gobj = update_giotto_params(temp_gobj, description = '_feats_perc')
Expand Down Expand Up @@ -1623,7 +1623,7 @@ addFeatsPerc = function(gobject,
#' @export
findNetworkNeighbors = function(gobject,
spat_unit = NULL,
spatial_network_name,
spatial_network_name = NULL,
source_cell_ids = NULL,
name = 'nb_cells') {

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