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update code after running lintr #4

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update code after running lintr #4

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d32e91a
update code after running lintr
hallvaaw Oct 20, 2022
fad9acb
fixed typos in installation commands
hallvaaw Oct 24, 2022
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6 changes: 3 additions & 3 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -48,8 +48,8 @@ devtools::install_github("GreenleafLab/ArchR",ref="master",repos=BiocManager::re
library(ArchR)
ArchR::installExtraPackages()

#Installing Required packages
install.packages(c("shiny","Seurat", "magick","hexbin","shinybusy","gridExtra", "grid","shinycssloaders")
#Installing Required packages
install.packages(c("shiny","Seurat", "magick","hexbin","shinybusy","gridExtra", "grid", "shinycssloaders"))
```
On command Line:

Expand All @@ -64,7 +64,7 @@ Rscript -e 'devtools::install_github("GreenleafLab/ArchR",ref="master",repos=Bi
Rscript -e 'ArchR::installExtraPackages()'

#Installs packages
Rscript -e 'install.packages(c("shiny","magick","hexbin","Seurat","shinybusy","gridExtra", "grid","shinycssloaders")'
Rscript -e 'install.packages(c("shiny","magick","hexbin","Seurat","shinybusy","gridExtra", "grid", "shinycssloaders"))'
```

### Adding folder paths and parameters
Expand Down
64 changes: 31 additions & 33 deletions global.R
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Original file line number Diff line number Diff line change
@@ -1,22 +1,22 @@
#####################################################################
# Setting up #
# Setting up #
#####################################################################
#updated:Feb102022
# if (!requireNamespace("Shiny", quietly = TRUE)) install.packages("shiny")
# ##Install ArchR,and its dependencies
# ##Install ArchR, and its dependencies
# #check for devtools
# if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
# #Install ArchR
# if (!requireNamespace("ArchR",quietly = TRUE)) devtools::install_github("GreenleafLab/ArchR",ref="master",repos=BiocManager::repositories())
# if (!requireNamespace("ArchR", quietly = TRUE)) devtools::install_github("GreenleafLab/ArchR", ref = "master", repos = BiocManager::repositories())
# #Install ArchR dependencies
# library(ArchR)
# ArchR::installExtraPackages()
# #Install presto
# if (!requireNamespace("presto",quietly = TRUE)) devtools::install_github("immunogenomics/presto")
# if (!requireNamespace("presto", quietly = TRUE)) devtools::install_github("immunogenomics/presto")

####
packages <- c("Seurat","shinycssloaders","hexbin","magick",
"gridExtra", "grid","patchwork","shinybusy","ArchR","ggseqlogo")
packages <- c("Seurat", "shinycssloaders", "hexbin", "magick",
"gridExtra", "grid", "patchwork", "shinybusy", "ArchR", "ggseqlogo")

## Now load or install&load all
package.check <- lapply(
Expand All @@ -32,10 +32,10 @@ package.check <- lapply(
options(repos = BiocManager::repositories())

#####################################################################
# Setting up ARCHR
# Setting up ARCHR
#####################################################################
#specify desired number of threads , If required
addArchRThreads(threads = 1)
addArchRThreads(threads = 1)
#specify genome version. Default hg19 set
addArchRGenome("hg19")
set.seed(1)
Expand All @@ -47,7 +47,7 @@ set.seed(1)
##Load the Saved projects folders from ArchR analysis as saved in ArchR full manual using saveArchRProject() function
#Load Saved-project folders path e.g 'Save-ArchRProject2'<- loadArchRProject("path/to/your/Save-ArchRProject2"). Save project also after trajectory analysis e.g as Save-ArchRProject5
#Please see ArchR full manual for saveArchRProject() function or use the ArchR.RMD for your analysis provided with the source code which follows the steps illustrated in ArchR full manual. Save-ArchRProject5
#
#
savedArchRProject1 <- loadArchRProject("~/ArchRAnalysis/Save-ProjHeme2/")
savedArchRProject2 <- loadArchRProject("~/ArchRAnalysis/Save-ProjHeme3/")
savedArchRProject3 <- loadArchRProject("~/ArchRAnalysis/Save-ProjHeme5/")
Expand All @@ -65,56 +65,56 @@ trajectory_name<-"LymphoidU"

cluster_umap <- plotEmbedding(
ArchRProj = savedArchRProject1,
baseSize=12,
baseSize = 12,
colorBy = "cellColData",
name = "Clusters",
embedding = "UMAP",
rastr = FALSE,
size=0.5,
size = 0.5,

)+ggtitle("Colored by scATAC-seq clusters")+theme(text=element_text(size=12), legend.title = element_text(size = 12),legend.text = element_text(size = 6))
) + ggtitle("Colored by scATAC-seq clusters") + theme(text = element_text(size = 12), legend.title = element_text(size = 12), legend.text = element_text(size = 6))

sample_umap <- plotEmbedding(
ArchRProj = savedArchRProject1,
baseSize=12,
baseSize = 12,
colorBy = "cellColData",
name = "Sample",
embedding = "UMAP",
rastr = FALSE,
size=0.5
)+ ggtitle("Colored by original identity")+theme(text=element_text(size=12), legend.title = element_text( size = 12),legend.text = element_text(size = 6))
size = 0.5
) + ggtitle("Colored by original identity") + theme(text = element_text(size = 12), legend.title = element_text( size = 12), legend.text = element_text(size = 6))

unconstrained_umap <- plotEmbedding(
ArchRProj = savedArchRProject1,
embedding = "UMAP",
reducedDims = "IterativeLSI",
colorBy = "cellColData",
name = "predictedGroup_Un",
baseSize=12,
baseSize = 12,

rastr = FALSE,
size=0.5
)+ggtitle("UMAP: unconstrained integration")+theme(text=element_text(size=12), legend.title = element_text( size = 12),legend.text = element_text(size = 6))
size = 0.5
) + ggtitle("UMAP: unconstrained integration") + theme(text = element_text(size = 12), legend.title = element_text( size = 12), legend.text = element_text(size = 6))

constrained_umap <- plotEmbedding(
ArchRProj = savedArchRProject1,
reducedDims = "IterativeLSI",
colorBy = "cellColData",
name = "predictedGroup_Co",
rastr = FALSE,
baseSize=12,
size=0.5
)+ggtitle("UMAP: constrained integration")+theme(text=element_text(size=12), legend.title = element_text( size = 12),legend.text = element_text(size = 6))
baseSize = 12,
size = 0.5
) + ggtitle("UMAP: constrained integration") + theme(text = element_text(size = 12), legend.title = element_text( size = 12), legend.text = element_text(size = 6))


constrained_remapped_umap <- plotEmbedding(
savedArchRProject2,
colorBy = "cellColData",
name = "Clusters2",
rastr = FALSE,
)+ggtitle("UMAP: Constrained remapped clusters")+theme(text=element_text(size=12), legend.title = element_text( size = 12),legend.text = element_text(size = 6))
) + ggtitle("UMAP: Constrained remapped clusters") + theme(text = element_text(size = 12), legend.title = element_text( size = 12), legend.text = element_text(size = 6))

umaps<-list("Clusters"= cluster_umap,"Sample"= sample_umap,"Unconstrained"=unconstrained_umap,"Constrained"=constrained_umap,"Constrained remap"=constrained_remapped_umap)
umaps <- list("Clusters" = cluster_umap, "Sample" = sample_umap, "Unconstrained" = unconstrained_umap, "Constrained" = constrained_umap, "Constrained remap" = constrained_remapped_umap)
########################################################################
# MarkerGenes
########################################################################
Expand All @@ -129,18 +129,18 @@ markersGS <- getMarkerFeatures(
bias = c("TSSEnrichment", "log10(nFrags)"),
testMethod = "wilcoxon"
)
markerList_p1 <- getMarkers(markersGS, cutOff = "FDR <= 0.1 & Log2FC >= 0.1")
markerList_p1 <- getMarkers(markersGS, cutOff = "FDR < = 0.1 & Log2FC > = 0.1")

# Find the all the genes available in the data
gene_names <- markerList_p1[[names(markerList_p1)[1]]]$name
for (cn in names(markerList_p1)[-1]){
gene_names <- union(gene_names,markerList_p1[[cn]]$name)
gene_names <- union(gene_names, markerList_p1[[cn]]$name)
}

########################################################################
# motifs for feature comparison panel
########################################################################
motifMatrix_forShiny=getMatrixFromProject(
motifMatrix_forShiny <- getMatrixFromProject(
ArchRProj = savedArchRProject3,
useMatrix = "MotifMatrix",
useSeqnames = NULL,
Expand All @@ -149,12 +149,12 @@ motifMatrix_forShiny=getMatrixFromProject(
threads = getArchRThreads()
)

#motifMatrix_dropdown=sapply(strsplit(motifMatrix_forShiny@NAMES, "_"), "[", 1)
motifMatrix_dropdown=motifMatrix_forShiny@NAMES

motifMatrix_dropdown <- motifMatrix_forShiny@NAMES

#get PWM of motifs and convert them to probability matrix for seqlogo:Utilized function from utils.R of https://github.com/GreenleafLab/ChrAccR
PWMatrixToProbMatrix <- function(x){
if (class(x) != "PWMatrix") stop("x must be a TFBSTools::PWMatrix object")
PWMatrixToProbMatrix <- function(x) {
if (class(x) != "PWMatrix") stop("x must be a TFBSTools::PWMatrix object")
(2^as(x, "matrix"))*TFBSTools::bg(x)/sum(TFBSTools::bg(x))
}

Expand All @@ -171,7 +171,7 @@ reducedDims <- "IterativeLSI"
########################################################################
# motif footprinting
########################################################################
motifPositions=getPositions(savedArchRProject3)
motifPositions <- getPositions(savedArchRProject3)
########################################################################
# Heatmap:Trajectory and peak2genelink
########################################################################
Expand All @@ -191,5 +191,3 @@ p_peakMatrix_traj <- plotTrajectoryHeatmap(trajPM, pal = paletteContinuous(set =
########################################################################
# End
########################################################################


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