Merge pull request #38 from genesofeve/projectionDriveR

Projection drive r

.lintr

@@ -0,0 +1,4 @@
+linters: all_linters()
+exclusions: list("projectR/tests/testthat/test_projectR.R",
+                 "projectR/tests/testthat.R")
+encoding: "UTF-8"

DESCRIPTION

@@ -4,7 +4,14 @@ Title: Functions for the projection of weights from PCA, CoGAPS, NMF,
     correlation, and clustering
 Version: 1.19.01
 Author: Gaurav Sharma, Charles Shin, Jared Slosberg, Loyal Goff, Genevieve Stein-O'Brien
-Maintainer: Genevieve Stein-O'Brien <gsteinobrien@gmail.com>
+Authors@R: c(
+    person("Gaurav", "Sharma", role = c("aut")),
+    person("Charles", "Shin", role = c("aut")),
+    person("Jared", "Slosberg", role = c("aut")),
+    person("Loyal", "Goff", role = c("aut")),
+    person("Ryan", "Palaganas", role = c("aut")),
+    person("Genevieve", "Stein-O'Brien", role = c("aut", "cre" ), email = "gsteinobrien@gmail.com")
+    )
 Description: Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.
 License: GPL (==2)
 Imports:
@@ -17,11 +24,13 @@ Imports:
     ggalluvial,
     RColorBrewer,
     dplyr,
+    fgsea,
     reshape2,
     viridis,
     scales,
     Matrix,
     MatrixModels,
+    msigdbr,
     ggplot2,
     cowplot,
     ggrepel,
@@ -41,7 +50,7 @@ Suggests:
     SeuratObject
 LazyData: TRUE
 LazyDataCompression: gzip
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 VignetteBuilder: knitr
 biocViews: FunctionalPrediction, GeneRegulation, BiologicalQuestion, Software

NAMESPACE

@@ -10,7 +10,9 @@ export(getTSNE)
 export(getUMAP)
 export(intersectoR)
 export(multivariateAnalysisR)
+export(pdVolcano)
 export(plotConfidenceIntervals)
+export(plotVolcano)
 export(projectR)
 export(projectionDriveR)
 export(rotatoR)
@@ -21,14 +23,17 @@ import(MatrixModels)
 import(RColorBrewer)
 import(cluster)
 import(dplyr)
+import(fgsea)
 import(ggalluvial)
 import(ggplot2)
 import(limma)
+import(msigdbr)
 import(reshape2)
 import(scales, except = viridis_pal)
 import(tsne)
 import(umap)
 import(viridis)
+importFrom(Matrix,as.matrix)
 importFrom(NMF,fcnnls)
 importFrom(ROCR,performance)
 importFrom(ROCR,prediction)
@@ -37,6 +42,7 @@ importFrom(dplyr,"%>%")
 importFrom(dplyr,dense_rank)
 importFrom(dplyr,mutate)
 importFrom(ggrepel,geom_label_repel)
+importFrom(ggrepel,geom_text_repel)
 importFrom(grDevices,colorRampPalette)
 importFrom(methods,callNextMethod)
 importFrom(scales,squish)

R/package.R

@@ -95,6 +95,16 @@
 #' @format A CogapsResult object
 "CR.RNAseq6l3c3t"
 
+#' CogapsResult object for microglial_counts
+#'
+#' cr_microglia contains the output of the CoGAPS function in the
+#' CoGAPS package for data = microglial_counts
+#'
+#' @name cr_microglial
+#' @docType data
+#' @format A CogapsResult object
+"cr_microglial"
+
 #' CoGAPS patterns learned from the developing mouse retina.
 #'
 #' @references