1. celda
  2. NAMESPACE
Browse code

Added subsampling parameters for perplexity calculation to recursive split functions

Joshua D. Campbell authored on 28/03/2022 12:00:25
Showing 1 changed files
NAMESPACE
History View file @ 7e5d8207
... ... 
@@ -125,6 +125,7 @@ import(grDevices)
125 125 
 import(graphics)
126 126 
 import(grid)
127 127 
 import(uwot)
128 
+importClassesFrom(Matrix,dgCMatrix)
128 129 
 importClassesFrom(SingleCellExperiment,SingleCellExperiment)
129 130 
 importFrom(MCMCprecision,fit_dirichlet)
130 131 
 importFrom(Matrix,colSums)
Browse code

Moved Matrix and SingleCellExperiment to Depends to make sure these are loaded when using celda

Joshua D. Campbell authored on 25/03/2022 20:25:48
Showing 1 changed files
NAMESPACE
History View file @ 7d788c93
... ... 
@@ -125,6 +125,7 @@ import(grDevices)
125 125 
 import(graphics)
126 126 
 import(grid)
127 127 
 import(uwot)
128 
+importClassesFrom(SingleCellExperiment,SingleCellExperiment)
128 129 
 importFrom(MCMCprecision,fit_dirichlet)
129 130 
 importFrom(Matrix,colSums)
130 131 
 importFrom(Matrix,rowSums)
Browse code

add displayName to featureModuleTable. Remove stringi

zhewa authored on 11/05/2021 15:10:13
Showing 1 changed files
NAMESPACE
History View file @ 3a9bde76
... ... 
@@ -156,7 +156,6 @@ importFrom(reshape2,melt)
156 156 
 importFrom(scales,brewer_pal)
157 157 
 importFrom(scales,dscale)
158 158 
 importFrom(scales,hue_pal)
159 
-importFrom(stringi,stri_list2matrix)
160 159 
 importFrom(withr,with_seed)
161 160 
 importMethodsFrom(Matrix,"%*%")
162 161 
 useDynLib(celda,"_colSumByGroup")
Browse code

fix error. Add alpha arg to perplexity plots

zhewa authored on 02/05/2021 14:45:48
Showing 1 changed files
NAMESPACE
History View file @ 48e12245
... ... 
@@ -47,8 +47,8 @@ export(plotDimReduceFeature)
47 47 
 export(plotDimReduceGrid)
48 48 
 export(plotDimReduceModule)
49 49 
 export(plotGridSearchPerplexity)
50 
-export(plotGridSearchPerplexityDiff)
51 50 
 export(plotHeatmap)
51 
+export(plotRPC)
52 52 
 export(recodeClusterY)
53 53 
 export(recodeClusterZ)
54 54 
 export(recursiveSplitCell)
... ... 
@@ -106,7 +106,7 @@ exportMethods(plotDimReduceFeature)
106 106 
 exportMethods(plotDimReduceGrid)
107 107 
 exportMethods(plotDimReduceModule)
108 108 
 exportMethods(plotGridSearchPerplexity)
109 
-exportMethods(plotGridSearchPerplexityDiff)
109 
+exportMethods(plotRPC)
110 110 
 exportMethods(recursiveSplitCell)
111 111 
 exportMethods(recursiveSplitModule)
112 112 
 exportMethods(reorderCelda)
Browse code

Merge branch 'devel' of github.com:campbio/celda into devel

zhewa authored on 27/04/2021 14:07:40
Showing 0 changed files
Browse code

replace setReplaceMethod. Remove findMarkersTree, getDecisions

zhewa authored on 20/04/2021 14:16:59
Showing 1 changed files
NAMESPACE
History View file @ 42ac786c
... ... 
@@ -30,9 +30,7 @@ export(distinctColors)
30 30 
 export(factorizeMatrix)
31 31 
 export(featureModuleLookup)
32 32 
 export(featureModuleTable)
33 
-export(findMarkersTree)
34 33 
 export(geneSetEnrich)
35 
-export(getDecisions)
36 34 
 export(logLikelihood)
37 35 
 export(logLikelihoodHistory)
38 36 
 export(matrixNames)
... ... 
@@ -51,8 +49,6 @@ export(plotDimReduceModule)
51 49 
 export(plotGridSearchPerplexity)
52 50 
 export(plotGridSearchPerplexityDiff)
53 51 
 export(plotHeatmap)
54 
-export(plotMarkerDendro)
55 
-export(plotMarkerHeatmap)
56 52 
 export(recodeClusterY)
57 53 
 export(recodeClusterZ)
58 54 
 export(recursiveSplitCell)
... ... 
@@ -97,7 +93,6 @@ exportMethods(decontX)
97 93 
 exportMethods(decontXcounts)
98 94 
 exportMethods(factorizeMatrix)
99 95 
 exportMethods(featureModuleLookup)
100 
-exportMethods(findMarkersTree)
101 96 
 exportMethods(geneSetEnrich)
102 97 
 exportMethods(logLikelihood)
103 98 
 exportMethods(logLikelihoodHistory)
Browse code

Refactored matrix multiplication with sparse matrices to a separate function. Fixed unit tests and one bug in recursiveModuleSplit

Joshua D. Campbell authored on 06/04/2021 02:13:59
Showing 1 changed files
NAMESPACE
History View file @ bd98acab
... ... 
@@ -131,6 +131,9 @@ import(graphics)
131 131 
 import(grid)
132 132 
 import(uwot)
133 133 
 importFrom(MCMCprecision,fit_dirichlet)
134 
+importFrom(Matrix,colSums)
135 
+importFrom(Matrix,rowSums)
136 
+importFrom(Matrix,t)
134 137 
 importFrom(RColorBrewer,brewer.pal)
135 138 
 importFrom(Rtsne,Rtsne)
136 139 
 importFrom(data.table,as.data.table)
... ... 
@@ -160,6 +163,7 @@ importFrom(scales,dscale)
160 163 
 importFrom(scales,hue_pal)
161 164 
 importFrom(stringi,stri_list2matrix)
162 165 
 importFrom(withr,with_seed)
166 
+importMethodsFrom(Matrix,"%*%")
163 167 
 useDynLib(celda,"_colSumByGroup")
164 168 
 useDynLib(celda,"_colSumByGroupChange")
165 169 
 useDynLib(celda,"_colSumByGroupChange_numeric")
Browse code

Fixed numeric matrix computations in celda_C. Added ability to use numeric and sparse matrices in celda_G and celda_CG

Joshua D. Campbell authored on 05/04/2021 02:40:50
Showing 1 changed files
NAMESPACE
History View file @ 09a819f3
... ... 
@@ -162,8 +162,10 @@ importFrom(stringi,stri_list2matrix)
162 162 
 importFrom(withr,with_seed)
163 163 
 useDynLib(celda,"_colSumByGroup")
164 164 
 useDynLib(celda,"_colSumByGroupChange")
165 
+useDynLib(celda,"_colSumByGroupChange_numeric")
165 166 
 useDynLib(celda,"_colSumByGroup_numeric")
166 167 
 useDynLib(celda,"_perplexityG")
167 168 
 useDynLib(celda,"_rowSumByGroup")
168 169 
 useDynLib(celda,"_rowSumByGroupChange")
170 
+useDynLib(celda,"_rowSumByGroupChange_numeric")
169 171 
 useDynLib(celda,"_rowSumByGroup_numeric")
Browse code

updated docs

Joshua D. Campbell authored on 30/03/2021 15:04:24
Showing 1 changed files
NAMESPACE
History View file @ 5474f6c3
... ... 
@@ -26,7 +26,6 @@ export(compareCountMatrix)
26 26 
 export(countChecksum)
27 27 
 export(decontX)
28 28 
 export(decontXcounts)
29 
-export(differentialExpression)
30 29 
 export(distinctColors)
31 30 
 export(factorizeMatrix)
32 31 
 export(featureModuleLookup)
... ... 
@@ -96,7 +95,6 @@ exportMethods(compareCountMatrix)
96 95 
 exportMethods(countChecksum)
97 96 
 exportMethods(decontX)
98 97 
 exportMethods(decontXcounts)
99 
-exportMethods(differentialExpression)
100 98 
 exportMethods(factorizeMatrix)
101 99 
 exportMethods(featureModuleLookup)
102 100 
 exportMethods(findMarkersTree)
... ... 
@@ -127,20 +125,14 @@ exportMethods(splitModule)
127 125 
 exportMethods(subsetCeldaList)
128 126 
 import(Rcpp)
129 127 
 import(RcppEigen)
130 
-import(SummarizedExperiment)
131 
-import(data.table, except = c(melt, shift))
132 128 
 import(foreach)
133 129 
 import(grDevices)
134 130 
 import(graphics)
135 131 
 import(grid)
136 132 
 import(uwot)
137 
-importFrom(MAST,FromMatrix)
138 
-importFrom(MAST,summary)
139 
-importFrom(MAST,zlm)
140 133 
 importFrom(MCMCprecision,fit_dirichlet)
141 134 
 importFrom(RColorBrewer,brewer.pal)
142 135 
 importFrom(Rtsne,Rtsne)
143 
-importFrom(S4Vectors,mcols)
144 136 
 importFrom(data.table,as.data.table)
145 137 
 importFrom(digest,digest)
146 138 
 importFrom(doParallel,registerDoParallel)
... ... 
@@ -161,7 +153,6 @@ importFrom(methods,.hasSlot)
161 153 
 importFrom(methods,is)
162 154 
 importFrom(methods,new)
163 155 
 importFrom(multipanelfigure,multi_panel_figure)
164 
-importFrom(plyr,.)
165 156 
 importFrom(plyr,mapvalues)
166 157 
 importFrom(reshape2,melt)
167 158 
 importFrom(scales,brewer_pal)
Browse code

Fixed documentation for reportCeldaCG functins

Joshua D. Campbell authored on 22/03/2021 13:24:24
Showing 1 changed files
NAMESPACE
History View file @ f40af422
... ... 
@@ -59,7 +59,8 @@ export(recodeClusterZ)
59 59 
 export(recursiveSplitCell)
60 60 
 export(recursiveSplitModule)
61 61 
 export(reorderCelda)
62 
-export(reportCeldaCG_PlotResults)
62 
+export(reportCeldaCGPlotResults)
63 
+export(reportCeldaCGRun)
63 64 
 export(resList)
64 65 
 export(resamplePerplexity)
65 66 
 export(retrieveFeatureIndex)
Browse code

add reorderCelda for sce objects

zhewa authored on 17/03/2021 18:28:35
Showing 1 changed files
NAMESPACE
History View file @ 44efa168
... ... 
@@ -58,6 +58,7 @@ export(recodeClusterY)
58 58 
 export(recodeClusterZ)
59 59 
 export(recursiveSplitCell)
60 60 
 export(recursiveSplitModule)
61 
+export(reorderCelda)
61 62 
 export(reportCeldaCG_PlotResults)
62 63 
 export(resList)
63 64 
 export(resamplePerplexity)
... ... 
@@ -114,6 +115,7 @@ exportMethods(plotGridSearchPerplexity)
114 115 
 exportMethods(plotGridSearchPerplexityDiff)
115 116 
 exportMethods(recursiveSplitCell)
116 117 
 exportMethods(recursiveSplitModule)
118 
+exportMethods(reorderCelda)
117 119 
 exportMethods(resList)
118 120 
 exportMethods(resamplePerplexity)
119 121 
 exportMethods(runParams)
Browse code

Modified report functions and rmarkdown

Joshua D. Campbell authored on 15/03/2021 18:46:04
Showing 1 changed files
NAMESPACE
History View file @ d461e4d9
... ... 
@@ -58,6 +58,7 @@ export(recodeClusterY)
58 58 
 export(recodeClusterZ)
59 59 
 export(recursiveSplitCell)
60 60 
 export(recursiveSplitModule)
61 
+export(reportCeldaCG_PlotResults)
61 62 
 export(resList)
62 63 
 export(resamplePerplexity)
63 64 
 export(retrieveFeatureIndex)
Browse code

upgrade probabilityMap

zhewa authored on 13/10/2020 00:14:45
Showing 1 changed files
NAMESPACE
History View file @ 16389352
... ... 
@@ -129,7 +129,6 @@ import(foreach)
129 129 
 import(grDevices)
130 130 
 import(graphics)
131 131 
 import(grid)
132 
-import(gridExtra, except = c(combine))
133 132 
 import(uwot)
134 133 
 importFrom(MAST,FromMatrix)
135 134 
 importFrom(MAST,summary)
... ... 
@@ -149,7 +148,6 @@ importFrom(grDevices,colors)
149 148 
 importFrom(grDevices,hsv)
150 149 
 importFrom(grDevices,rgb2hsv)
151 150 
 importFrom(grid,grid.pretty)
152 
-importFrom(gridExtra,grid.arrange)
153 151 
 importFrom(gtable,gtable)
154 152 
 importFrom(gtable,gtable_add_grob)
155 153 
 importFrom(gtable,gtable_height)
... ... 
@@ -158,6 +156,7 @@ importFrom(matrixStats,logSumExp)
158 156 
 importFrom(methods,.hasSlot)
159 157 
 importFrom(methods,is)
160 158 
 importFrom(methods,new)
159 
+importFrom(multipanelfigure,multi_panel_figure)
161 160 
 importFrom(plyr,.)
162 161 
 importFrom(plyr,mapvalues)
163 162 
 importFrom(reshape2,melt)
Browse code

update celdatosce, celda.rmd

zhewa authored on 10/10/2020 17:01:35
Showing 1 changed files
NAMESPACE
History View file @ 53bd7c8d
... ... 
@@ -89,6 +89,7 @@ exportMethods(celda_CG)
89 89 
 exportMethods(celda_G)
90 90 
 exportMethods(celdatosce)
91 91 
 exportMethods(clusterProbability)
92 
+exportMethods(compareCountMatrix)
92 93 
 exportMethods(countChecksum)
93 94 
 exportMethods(decontX)
94 95 
 exportMethods(decontXcounts)
Browse code

update doc

zhewa authored on 29/09/2020 22:05:25
Showing 1 changed files
NAMESPACE
History View file @ 27eecae0
... ... 
@@ -129,7 +129,6 @@ import(grDevices)
129 129 
 import(graphics)
130 130 
 import(grid)
131 131 
 import(gridExtra, except = c(combine))
132 
-import(patchwork)
133 132 
 import(uwot)
134 133 
 importFrom(MAST,FromMatrix)
135 134 
 importFrom(MAST,summary)
Browse code

multiple moduleHeatmap on same page. remove blank page

zhewa authored on 16/09/2020 15:50:01
Showing 1 changed files
NAMESPACE
History View file @ 1d563e1f
... ... 
@@ -129,6 +129,7 @@ import(grDevices)
129 129 
 import(graphics)
130 130 
 import(grid)
131 131 
 import(gridExtra, except = c(combine))
132 
+import(patchwork)
132 133 
 import(uwot)
133 134 
 importFrom(MAST,FromMatrix)
134 135 
 importFrom(MAST,summary)
Browse code

add altExpName = "featureSubset". Store results in altExp(sce)

zhewa authored on 13/07/2020 06:58:29
Showing 1 changed files
NAMESPACE
History View file @ 898ab9e0
... ... 
@@ -64,6 +64,7 @@ export(retrieveFeatureIndex)
64 64 
 export(runParams)
65 65 
 export(sampleLabel)
66 66 
 export(selectBestModel)
67 
+export(selectFeatures)
67 68 
 export(simulateCells)
68 69 
 export(simulateContamination)
69 70 
 export(splitModule)
... ... 
@@ -116,6 +117,7 @@ exportMethods(resamplePerplexity)
116 117 
 exportMethods(runParams)
117 118 
 exportMethods(sampleLabel)
118 119 
 exportMethods(selectBestModel)
120 
+exportMethods(selectFeatures)
119 121 
 exportMethods(splitModule)
120 122 
 exportMethods(subsetCeldaList)
121 123 
 import(Rcpp)
Browse code

add splitModule, a function to manually split feature module

zhewa authored on 17/06/2020 13:02:02
Showing 1 changed files
NAMESPACE
History View file @ f9b287b4
... ... 
@@ -66,6 +66,7 @@ export(sampleLabel)
66 66 
 export(selectBestModel)
67 67 
 export(simulateCells)
68 68 
 export(simulateContamination)
69 
+export(splitModule)
69 70 
 export(subsetCeldaList)
70 71 
 export(topRank)
71 72 
 exportMethods("celdaClusters<-")
... ... 
@@ -115,6 +116,7 @@ exportMethods(resamplePerplexity)
115 116 
 exportMethods(runParams)
116 117 
 exportMethods(sampleLabel)
117 118 
 exportMethods(selectBestModel)
119 
+exportMethods(splitModule)
118 120 
 exportMethods(subsetCeldaList)
119 121 
 import(Rcpp)
120 122 
 import(RcppEigen)
Browse code

add plotGridSearchPerplexityDiff, add as.matrix(counts) to .processCounts

zhewa authored on 01/06/2020 12:40:35
Showing 1 changed files
NAMESPACE
History View file @ 329ba8b9
... ... 
@@ -50,6 +50,7 @@ export(plotDimReduceFeature)
50 50 
 export(plotDimReduceGrid)
51 51 
 export(plotDimReduceModule)
52 52 
 export(plotGridSearchPerplexity)
53 
+export(plotGridSearchPerplexityDiff)
53 54 
 export(plotHeatmap)
54 55 
 export(plotMarkerDendro)
55 56 
 export(plotMarkerHeatmap)
... ... 
@@ -106,6 +107,7 @@ exportMethods(plotDimReduceFeature)
106 107 
 exportMethods(plotDimReduceGrid)
107 108 
 exportMethods(plotDimReduceModule)
108 109 
 exportMethods(plotGridSearchPerplexity)
110 
+exportMethods(plotGridSearchPerplexityDiff)
109 111 
 exportMethods(recursiveSplitCell)
110 112 
 exportMethods(recursiveSplitModule)
111 113 
 exportMethods(resList)
Browse code

update docs

zhewa authored on 21/05/2020 09:04:10
Showing 1 changed files
NAMESPACE
History View file @ 05a1113d
... ... 
@@ -1,16 +1,18 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export("clusters<-")
3 
+export("celdaClusters<-")
4 
+export("celdaModules<-")
4 5 
 export("decontXcounts<-")
5 
-export("modules<-")
6 6 
 export("sampleLabel<-")
7 7 
 export(appendCeldaList)
8 8 
 export(availableModels)
9 9 
 export(bestLogLikelihood)
10 10 
 export(celda)
11 
+export(celdaClusters)
11 12 
 export(celdaGridSearch)
12 13 
 export(celdaHeatmap)
13 14 
 export(celdaModel)
15 
+export(celdaModules)
14 16 
 export(celdaPerplexity)
15 17 
 export(celdaProbabilityMap)
16 18 
 export(celdaTsne)
... ... 
@@ -20,7 +22,6 @@ export(celda_CG)
20 22 
 export(celda_G)
21 23 
 export(celdatosce)
22 24 
 export(clusterProbability)
23 
-export(clusters)
24 25 
 export(compareCountMatrix)
25 26 
 export(countChecksum)
26 27 
 export(decontX)
... ... 
@@ -37,7 +38,6 @@ export(logLikelihood)
37 38 
 export(logLikelihoodHistory)
38 39 
 export(matrixNames)
39 40 
 export(moduleHeatmap)
40 
-export(modules)
41 41 
 export(normalizeCounts)
42 42 
 export(params)
43 43 
 export(perplexity)
... ... 
@@ -50,9 +50,6 @@ export(plotDimReduceFeature)
50 50 
 export(plotDimReduceGrid)
51 51 
 export(plotDimReduceModule)
52 52 
 export(plotGridSearchPerplexity)
53 
-export(plotGridSearchPerplexitycelda_C)
54 
-export(plotGridSearchPerplexitycelda_CG)
55 
-export(plotGridSearchPerplexitycelda_G)
56 53 
 export(plotHeatmap)
57 54 
 export(plotMarkerDendro)
58 55 
 export(plotMarkerHeatmap)
... ... 
@@ -70,14 +67,16 @@ export(simulateCells)
70 67 
 export(simulateContamination)
71 68 
 export(subsetCeldaList)
72 69 
 export(topRank)
73 
-exportMethods("clusters<-")
70 
+exportMethods("celdaClusters<-")
71 
+exportMethods("celdaModules<-")
74 72 
 exportMethods("decontXcounts<-")
75 
-exportMethods("modules<-")
76 73 
 exportMethods("sampleLabel<-")
77 74 
 exportMethods(bestLogLikelihood)
75 
+exportMethods(celdaClusters)
78 76 
 exportMethods(celdaGridSearch)
79 77 
 exportMethods(celdaHeatmap)
80 78 
 exportMethods(celdaModel)
79 
+exportMethods(celdaModules)
81 80 
 exportMethods(celdaPerplexity)
82 81 
 exportMethods(celdaProbabilityMap)
83 82 
 exportMethods(celdaTsne)
... ... 
@@ -87,19 +86,30 @@ exportMethods(celda_CG)
87 86 
 exportMethods(celda_G)
88 87 
 exportMethods(celdatosce)
89 88 
 exportMethods(clusterProbability)
90 
-exportMethods(clusters)
91 89 
 exportMethods(countChecksum)
92 90 
 exportMethods(decontX)
93 91 
 exportMethods(decontXcounts)
92 
+exportMethods(differentialExpression)
94 93 
 exportMethods(factorizeMatrix)
95 94 
 exportMethods(featureModuleLookup)
95 
+exportMethods(findMarkersTree)
96 
+exportMethods(geneSetEnrich)
96 97 
 exportMethods(logLikelihood)
97 98 
 exportMethods(logLikelihoodHistory)
98 99 
 exportMethods(matrixNames)
99 
-exportMethods(modules)
100 
+exportMethods(moduleHeatmap)
100 101 
 exportMethods(params)
101 102 
 exportMethods(perplexity)
103 
+exportMethods(plotCeldaViolin)
104 
+exportMethods(plotDimReduceCluster)
105 
+exportMethods(plotDimReduceFeature)
106 
+exportMethods(plotDimReduceGrid)
107 
+exportMethods(plotDimReduceModule)
108 
+exportMethods(plotGridSearchPerplexity)
109 
+exportMethods(recursiveSplitCell)
110 
+exportMethods(recursiveSplitModule)
102 111 
 exportMethods(resList)
112 
+exportMethods(resamplePerplexity)
103 113 
 exportMethods(runParams)
104 114 
 exportMethods(sampleLabel)
105 115 
 exportMethods(selectBestModel)
... ... 
@@ -121,9 +131,6 @@ importFrom(MCMCprecision,fit_dirichlet)
121 131 
 importFrom(RColorBrewer,brewer.pal)
122 132 
 importFrom(Rtsne,Rtsne)
123 133 
 importFrom(S4Vectors,mcols)
124 
-importFrom(SummarizedExperiment,assay)
125 
-importFrom(SummarizedExperiment,assayNames)
126 
-importFrom(SummarizedExperiment,colData)
127 134 
 importFrom(data.table,as.data.table)
128 135 
 importFrom(digest,digest)
129 136 
 importFrom(doParallel,registerDoParallel)
Browse code

selectBestModel

zhewa authored on 12/05/2020 11:14:38
Showing 1 changed files
NAMESPACE
History View file @ 4ec87fac
... ... 
@@ -102,6 +102,7 @@ exportMethods(perplexity)
102 102 
 exportMethods(resList)
103 103 
 exportMethods(runParams)
104 104 
 exportMethods(sampleLabel)
105 
+exportMethods(selectBestModel)
105 106 
 exportMethods(subsetCeldaList)
106 107 
 import(Rcpp)
107 108 
 import(RcppEigen)
Browse code

celdatosce subsetCeldaList

zhewa authored on 12/05/2020 07:41:33
Showing 1 changed files
NAMESPACE
History View file @ 2ec6775a
... ... 
@@ -18,6 +18,7 @@ export(celdaUmap)
18 18 
 export(celda_C)
19 19 
 export(celda_CG)
20 20 
 export(celda_G)
21 
+export(celdatosce)
21 22 
 export(clusterProbability)
22 23 
 export(clusters)
23 24 
 export(compareCountMatrix)
... ... 
@@ -67,6 +68,7 @@ export(sampleLabel)
67 68 
 export(selectBestModel)
68 69 
 export(simulateCells)
69 70 
 export(simulateContamination)
71 
+export(subsetCeldaList)
70 72 
 export(topRank)
71 73 
 exportMethods("clusters<-")
72 74 
 exportMethods("decontXcounts<-")
... ... 
@@ -83,6 +85,7 @@ exportMethods(celdaUmap)
83 85 
 exportMethods(celda_C)
84 86 
 exportMethods(celda_CG)
85 87 
 exportMethods(celda_G)
88 
+exportMethods(celdatosce)
86 89 
 exportMethods(clusterProbability)
87 90 
 exportMethods(clusters)
88 91 
 exportMethods(countChecksum)
... ... 
@@ -99,6 +102,7 @@ exportMethods(perplexity)
99 102 
 exportMethods(resList)
100 103 
 exportMethods(runParams)
101 104 
 exportMethods(sampleLabel)
105 
+exportMethods(subsetCeldaList)
102 106 
 import(Rcpp)
103 107 
 import(RcppEigen)
104 108 
 import(SummarizedExperiment)
Browse code

sce celdaGridSearch

zhewa authored on 12/05/2020 06:07:15
Showing 1 changed files
NAMESPACE
History View file @ c256b4af
... ... 
@@ -1,5 +1,104 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export("clusters<-")
4 
+export("decontXcounts<-")
5 
+export("modules<-")
6 
+export("sampleLabel<-")
7 
+export(appendCeldaList)
8 
+export(availableModels)
9 
+export(bestLogLikelihood)
10 
+export(celda)
11 
+export(celdaGridSearch)
12 
+export(celdaHeatmap)
13 
+export(celdaModel)
14 
+export(celdaPerplexity)
15 
+export(celdaProbabilityMap)
16 
+export(celdaTsne)
17 
+export(celdaUmap)
18 
+export(celda_C)
19 
+export(celda_CG)
20 
+export(celda_G)
21 
+export(clusterProbability)
22 
+export(clusters)
23 
+export(compareCountMatrix)
24 
+export(countChecksum)
25 
+export(decontX)
26 
+export(decontXcounts)
27 
+export(differentialExpression)
28 
+export(distinctColors)
29 
+export(factorizeMatrix)
30 
+export(featureModuleLookup)
31 
+export(featureModuleTable)
32 
+export(findMarkersTree)
33 
+export(geneSetEnrich)
34 
+export(getDecisions)
35 
+export(logLikelihood)
36 
+export(logLikelihoodHistory)
37 
+export(matrixNames)
38 
+export(moduleHeatmap)
39 
+export(modules)
40 
+export(normalizeCounts)
41 
+export(params)
42 
+export(perplexity)
43 
+export(plotCeldaViolin)
44 
+export(plotDecontXContamination)
45 
+export(plotDecontXMarkerExpression)
46 
+export(plotDecontXMarkerPercentage)
47 
+export(plotDimReduceCluster)
48 
+export(plotDimReduceFeature)
49 
+export(plotDimReduceGrid)
50 
+export(plotDimReduceModule)
51 
+export(plotGridSearchPerplexity)
52 
+export(plotGridSearchPerplexitycelda_C)
53 
+export(plotGridSearchPerplexitycelda_CG)
54 
+export(plotGridSearchPerplexitycelda_G)
55 
+export(plotHeatmap)
56 
+export(plotMarkerDendro)
57 
+export(plotMarkerHeatmap)
58 
+export(recodeClusterY)
59 
+export(recodeClusterZ)
60 
+export(recursiveSplitCell)
61 
+export(recursiveSplitModule)
62 
+export(resList)
63 
+export(resamplePerplexity)
64 
+export(retrieveFeatureIndex)
65 
+export(runParams)
66 
+export(sampleLabel)
67 
+export(selectBestModel)
68 
+export(simulateCells)
69 
+export(simulateContamination)
70 
+export(topRank)
71 
+exportMethods("clusters<-")
72 
+exportMethods("decontXcounts<-")
73 
+exportMethods("modules<-")
74 
+exportMethods("sampleLabel<-")
75 
+exportMethods(bestLogLikelihood)
76 
+exportMethods(celdaGridSearch)
77 
+exportMethods(celdaHeatmap)
78 
+exportMethods(celdaModel)
79 
+exportMethods(celdaPerplexity)
80 
+exportMethods(celdaProbabilityMap)
81 
+exportMethods(celdaTsne)
82 
+exportMethods(celdaUmap)
83 
+exportMethods(celda_C)
84 
+exportMethods(celda_CG)
85 
+exportMethods(celda_G)
86 
+exportMethods(clusterProbability)
87 
+exportMethods(clusters)
88 
+exportMethods(countChecksum)
89 
+exportMethods(decontX)
90 
+exportMethods(decontXcounts)
91 
+exportMethods(factorizeMatrix)
92 
+exportMethods(featureModuleLookup)
93 
+exportMethods(logLikelihood)
94 
+exportMethods(logLikelihoodHistory)
95 
+exportMethods(matrixNames)
96 
+exportMethods(modules)
97 
+exportMethods(params)
98 
+exportMethods(perplexity)
99 
+exportMethods(resList)
100 
+exportMethods(runParams)
101 
+exportMethods(sampleLabel)
3 102 
 import(Rcpp)
4 103 
 import(RcppEigen)
5 104 
 import(SummarizedExperiment)
Browse code

sce celdaGridSearch update docs

zhewa authored on 10/05/2020 13:27:03
Showing 1 changed files
NAMESPACE
History View file @ 15fa63f1
... ... 
@@ -1,97 +1,5 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export("decontXcounts<-")
4 
-export(appendCeldaList)
5 
-export(availableModels)
6 
-export(bestLogLikelihood)
7 
-export(celda)
8 
-export(celdaGridSearch)
9 
-export(celdaHeatmap)
10 
-export(celdaPerplexity)
11 
-export(celdaProbabilityMap)
12 
-export(celdaTsne)
13 
-export(celdaUmap)
14 
-export(celda_C)
15 
-export(celda_CG)
16 
-export(celda_G)
17 
-export(clusterProbability)
18 
-export(clusters)
19 
-export(compareCountMatrix)
20 
-export(countChecksum)
21 
-export(decontX)
22 
-export(decontXcounts)
23 
-export(differentialExpression)
24 
-export(distinctColors)
25 
-export(factorizeMatrix)
26 
-export(featureModuleLookup)
27 
-export(featureModuleTable)
28 
-export(findMarkersTree)
29 
-export(geneSetEnrich)
30 
-export(getDecisions)
31 
-export(logLikelihood)
32 
-export(logLikelihoodHistory)
33 
-export(logLikelihoodcelda_C)
34 
-export(logLikelihoodcelda_CG)
35 
-export(logLikelihoodcelda_G)
36 
-export(matrixNames)
37 
-export(moduleHeatmap)
38 
-export(normalizeCounts)
39 
-export(params)
40 
-export(perplexity)
41 
-export(plotCeldaViolin)
42 
-export(plotDecontXContamination)
43 
-export(plotDecontXMarkerExpression)
44 
-export(plotDecontXMarkerPercentage)
45 
-export(plotDimReduceCluster)
46 
-export(plotDimReduceFeature)
47 
-export(plotDimReduceGrid)
48 
-export(plotDimReduceModule)
49 
-export(plotGridSearchPerplexity)
50 
-export(plotGridSearchPerplexitycelda_C)
51 
-export(plotGridSearchPerplexitycelda_CG)
52 
-export(plotGridSearchPerplexitycelda_G)
53 
-export(plotHeatmap)
54 
-export(plotMarkerDendro)
55 
-export(plotMarkerHeatmap)
56 
-export(recodeClusterY)
57 
-export(recodeClusterZ)
58 
-export(recursiveSplitCell)
59 
-export(recursiveSplitModule)
60 
-export(resList)
61 
-export(resamplePerplexity)
62 
-export(retrieveFeatureIndex)
63 
-export(runParams)
64 
-export(sampleLabel)
65 
-export(selectBestModel)
66 
-export(simulateCells)
67 
-export(simulateCellscelda_C)
68 
-export(simulateCellscelda_CG)
69 
-export(simulateCellscelda_G)
70 
-export(simulateContamination)
71 
-export(subsetCeldaList)
72 
-export(topRank)
73 
-exportMethods("decontXcounts<-")
74 
-exportMethods(bestLogLikelihood)
75 
-exportMethods(celdaHeatmap)
76 
-exportMethods(celdaPerplexity)
77 
-exportMethods(celdaProbabilityMap)
78 
-exportMethods(celdaTsne)
79 
-exportMethods(celdaUmap)
80 
-exportMethods(celda_C)
81 
-exportMethods(clusterProbability)
82 
-exportMethods(clusters)
83 
-exportMethods(countChecksum)
84 
-exportMethods(decontX)
85 
-exportMethods(decontXcounts)
86 
-exportMethods(factorizeMatrix)
87 
-exportMethods(featureModuleLookup)
88 
-exportMethods(logLikelihoodHistory)
89 
-exportMethods(matrixNames)
90 
-exportMethods(params)
91 
-exportMethods(perplexity)
92 
-exportMethods(resList)
93 
-exportMethods(runParams)
94 
-exportMethods(sampleLabel)
95 3 
 import(Rcpp)
96 4 
 import(RcppEigen)
97 5 
 import(SummarizedExperiment)
... ... 
@@ -101,7 +9,6 @@ import(grDevices)
101 9 
 import(graphics)
102 10 
 import(grid)
103 11 
 import(gridExtra, except = c(combine))
104 
-import(stats, except = c(start, end))
105 12 
 import(uwot)
106 13 
 importFrom(MAST,FromMatrix)
107 14 
 importFrom(MAST,summary)
Browse code

Merge branch 'master' of https://github.com/campbio/celda into sce

zhewa authored on 07/04/2020 06:50:40
Showing 0 changed files
Browse code

Finalized DecontX expression violin plot function and vignette.

Joshua D. Campbell authored on 06/04/2020 04:17:58
Showing 1 changed files
NAMESPACE
History View file @ 51477d47
... ... 
@@ -38,8 +38,10 @@ export(moduleHeatmap)
38 38 
 export(normalizeCounts)
39 39 
 export(params)
40 40 
 export(perplexity)
41 
+export(plotCeldaViolin)
41 42 
 export(plotDecontXContamination)
42 
-export(plotDecontXMarkers)
43 
+export(plotDecontXMarkerExpression)
44 
+export(plotDecontXMarkerPercentage)
43 45 
 export(plotDimReduceCluster)
44 46 
 export(plotDimReduceFeature)
45 47 
 export(plotDimReduceGrid)
... ... 
@@ -68,7 +70,6 @@ export(simulateCellscelda_G)
68 70 
 export(simulateContamination)
69 71 
 export(subsetCeldaList)
70 72 
 export(topRank)
71 
-export(violinPlot)
72 73 
 exportMethods("decontXcounts<-")
73 74 
 exportMethods(bestLogLikelihood)
74 75 
 exportMethods(celdaHeatmap)
... ... 
@@ -95,7 +96,6 @@ import(RcppEigen)
95 96 
 import(SummarizedExperiment)
96 97 
 import(data.table, except = c(melt, shift))
97 98 
 import(foreach)
98 
-import(ggplot2)
99 99 
 import(grDevices)
100 100 
 import(graphics)
101 101 
 import(grid)
... ... 
@@ -123,7 +123,6 @@ importFrom(grDevices,colors)
123 123 
 importFrom(grDevices,hsv)
124 124 
 importFrom(grDevices,rgb2hsv)
125 125 
 importFrom(grid,grid.pretty)
126 
-importFrom(grid,unit)
127 126 
 importFrom(gridExtra,grid.arrange)
128 127 
 importFrom(gtable,gtable)
129 128 
 importFrom(gtable,gtable_add_grob)
Browse code

Major updates to DecontX. Developed new barplot and UMAP functions. Changed initialization to use UMAP from scater. Updated docs. Modified DexontX vignette to analyze PBMC4k. Added function to find features in a matrix or SCE object

Joshua D. Campbell authored on 02/04/2020 15:38:28
Showing 1 changed files
NAMESPACE
History View file @ ca89b777
... ... 
@@ -19,7 +19,6 @@ export(clusters)
19 19 
 export(compareCountMatrix)
20 20 
 export(countChecksum)
21 21 
 export(decontX)
22 
-export(decontXMarkerPlot)
23 22 
 export(decontXcounts)
24 23 
 export(differentialExpression)
25 24 
 export(distinctColors)
... ... 
@@ -39,6 +38,8 @@ export(moduleHeatmap)
39 38 
 export(normalizeCounts)
40 39 
 export(params)
41 40 
 export(perplexity)
41 
+export(plotDecontXContamination)
42 
+export(plotDecontXMarkers)
42 43 
 export(plotDimReduceCluster)
43 44 
 export(plotDimReduceFeature)
44 45 
 export(plotDimReduceGrid)
... ... 
@@ -56,6 +57,7 @@ export(recursiveSplitCell)
56 57 
 export(recursiveSplitModule)
57 58 
 export(resList)
58 59 
 export(resamplePerplexity)
60 
+export(retrieveFeatureIndex)
59 61 
 export(runParams)
60 62 
 export(sampleLabel)
61 63 
 export(selectBestModel)
... ... 
@@ -63,7 +65,7 @@ export(simulateCells)
63 65 
 export(simulateCellscelda_C)
64 66 
 export(simulateCellscelda_CG)
65 67 
 export(simulateCellscelda_G)
66 
-export(simulateContaminatedMatrix)
68 
+export(simulateContamination)
67 69 
 export(subsetCeldaList)
68 70 
 export(topRank)
69 71 
 export(violinPlot)
Browse code

rewrite celda_C to S4 dispatcher methods

zhewa authored on 21/03/2020 08:38:32
Showing 1 changed files
NAMESPACE
History View file @ c16ac252
... ... 
@@ -74,6 +74,7 @@ exportMethods(celdaPerplexity)
74 74 
 exportMethods(celdaProbabilityMap)
75 75 
 exportMethods(celdaTsne)
76 76 
 exportMethods(celdaUmap)
77 
+exportMethods(celda_C)
77 78 
 exportMethods(clusterProbability)
78 79 
 exportMethods(clusters)
79 80 
 exportMethods(countChecksum)
Browse code

Merged findMarkersTree

Joshua D. Campbell authored on 13/03/2020 03:03:26
Showing 0 changed files
Browse code

merged vignette fixes

Joshua D. Campbell authored on 13/03/2020 00:44:31
Showing 0 changed files
Browse code

still decontx plot etc

syyang authored on 10/03/2020 01:25:44
Showing 1 changed files
NAMESPACE
History View file @ fd34cee1
... ... 
@@ -7,7 +7,6 @@ export(bestLogLikelihood)
7 7 
 export(celda)
8 8 
 export(celdaGridSearch)
9 9 
 export(celdaHeatmap)
10 
-export(celdaMarkerPlot)
11 10 
 export(celdaPerplexity)
12 11 
 export(celdaProbabilityMap)
13 12 
 export(celdaTsne)
... ... 
@@ -20,6 +19,7 @@ export(clusters)
20 19 
 export(compareCountMatrix)
21 20 
 export(countChecksum)
22 21 
 export(decontX)
22 
+export(decontXMarkerPlot)
23 23 
 export(decontXcounts)
24 24 
 export(differentialExpression)
25 25 
 export(distinctColors)
Browse code

fix bug

zhewa authored on 05/03/2020 06:32:21
Showing 1 changed files
NAMESPACE
History View file @ bdb26ed8
... ... 
@@ -107,6 +107,7 @@ importFrom(MAST,summary)
107 107 
 importFrom(MAST,zlm)
108 108 
 importFrom(MCMCprecision,fit_dirichlet)
109 109 
 importFrom(RColorBrewer,brewer.pal)
110 
+importFrom(Ringo,nonzero)
110 111 
 importFrom(Rtsne,Rtsne)
111 112 
 importFrom(S4Vectors,mcols)
112 113 
 importFrom(SummarizedExperiment,assay)
Browse code

Updated docs. Fixed package referncing in celdaMarkerPlot. Updated DESCRIPTION.

Joshua D. Campbell authored on 02/03/2020 04:51:11
Showing 1 changed files
NAMESPACE
History View file @ 8374c3f6
... ... 
@@ -87,7 +87,6 @@ exportMethods(perplexity)
87 87 
 exportMethods(resList)
88 88 
 exportMethods(runParams)
89 89 
 exportMethods(sampleLabel)
90 
-import(Matrix)
91 90 
 import(Rcpp)
92 91 
 import(RcppEigen)
93 92 
 import(SummarizedExperiment)
Browse code

check whether ringo imports biocneighbors

syyang authored on 01/03/2020 18:21:23
Showing 1 changed files
NAMESPACE
History View file @ 8fd7a33e
... ... 
@@ -106,7 +106,6 @@ importFrom(MAST,summary)
106 106 
 importFrom(MAST,zlm)
107 107 
 importFrom(MCMCprecision,fit_dirichlet)
108 108 
 importFrom(RColorBrewer,brewer.pal)
109 
-importFrom(Ringo,nonzero)
110 109 
 importFrom(Rtsne,Rtsne)
111 110 
 importFrom(S4Vectors,mcols)
112 111 
 importFrom(SummarizedExperiment,assay)
Browse code

namespace

syyang authored on 01/03/2020 17:21:40
Showing 1 changed files
NAMESPACE
History View file @ b54c3d7d
... ... 
@@ -106,6 +106,7 @@ importFrom(MAST,summary)
106 106 
 importFrom(MAST,zlm)
107 107 
 importFrom(MCMCprecision,fit_dirichlet)
108 108 
 importFrom(RColorBrewer,brewer.pal)
109 
+importFrom(Ringo,nonzero)
109 110 
 importFrom(Rtsne,Rtsne)
110 111 
 importFrom(S4Vectors,mcols)
111 112 
 importFrom(SummarizedExperiment,assay)
Browse code

documentation

syyang authored on 29/02/2020 22:45:48
Showing 1 changed files
NAMESPACE
History View file @ d2f898d9
... ... 
@@ -7,6 +7,7 @@ export(bestLogLikelihood)
7 7 
 export(celda)
8 8 
 export(celdaGridSearch)
9 9 
 export(celdaHeatmap)
10 
+export(celdaMarkerPlot)
10 11 
 export(celdaPerplexity)
11 12 
 export(celdaProbabilityMap)
12 13 
 export(celdaTsne)
... ... 
@@ -86,6 +87,7 @@ exportMethods(perplexity)
86 87 
 exportMethods(resList)
87 88 
 exportMethods(runParams)
88 89 
 exportMethods(sampleLabel)
90 
+import(Matrix)
89 91 
 import(Rcpp)
90 92 
 import(RcppEigen)
91 93 
 import(SummarizedExperiment)
Browse code

Updated markertree functions and documentation

Joshua D. Campbell authored on 11/02/2020 02:36:33
Showing 1 changed files
NAMESPACE
History View file @ e01eb3e9
... ... 
@@ -37,7 +37,6 @@ export(moduleHeatmap)
37 37 
 export(normalizeCounts)
38 38 
 export(params)
39 39 
 export(perplexity)
40 
-export(plotDendro)
41 40 
 export(plotDimReduceCluster)
42 41 
 export(plotDimReduceFeature)
43 42 
 export(plotDimReduceGrid)
... ... 
@@ -47,6 +46,7 @@ export(plotGridSearchPerplexitycelda_C)
47 46 
 export(plotGridSearchPerplexitycelda_CG)
48 47 
 export(plotGridSearchPerplexitycelda_G)
49 48 
 export(plotHeatmap)
49 
+export(plotMarkerDendro)
50 50 
 export(plotMarkerHeatmap)
51 51 
 export(recodeClusterY)
52 52 
 export(recodeClusterZ)
... ... 
@@ -96,7 +96,6 @@ import(grDevices)
96 96 
 import(graphics)
97 97 
 import(grid)
98 98 
 import(gridExtra, except = c(combine))
99 
-import(magrittr)
100 99 
 import(stats, except = c(start, end))
101 100 
 import(uwot)
102 101 
 importFrom(MAST,FromMatrix)
Browse code

Fixed marker tree build errors

Joshua D. Campbell authored on 09/02/2020 20:45:56
Showing 1 changed files
NAMESPACE
History View file @ 4e4af3ea
... ... 
@@ -90,7 +90,6 @@ import(Rcpp)
90 90 
 import(RcppEigen)
91 91 
 import(SummarizedExperiment)
92 92 
 import(data.table, except = c(melt, shift))
93 
-import(dbscan)
94 93 
 import(foreach)
95 94 
 import(ggplot2)
96 95 
 import(grDevices)
... ... 
@@ -98,10 +97,8 @@ import(graphics)
98 97 
 import(grid)
99 98 
 import(gridExtra, except = c(combine))
100 99 
 import(magrittr)
101 
-import(pROC)
102 100 
 import(stats, except = c(start, end))
103 101 
 import(uwot)
104 
-import(withr)
105 102 
 importFrom(MAST,FromMatrix)
106 103 
 importFrom(MAST,summary)
107 104 
 importFrom(MAST,zlm)
... ... 
@@ -113,15 +110,10 @@ importFrom(SummarizedExperiment,assay)
113 110 
 importFrom(SummarizedExperiment,assayNames)
114 111 
 importFrom(SummarizedExperiment,colData)
115 112 
 importFrom(data.table,as.data.table)
116 
-importFrom(dendextend,get_leaves_attr)
117 
-importFrom(dendextend,get_nodes_attr)
118 
-importFrom(dendextend,get_nodes_xy)
119 113 
 importFrom(digest,digest)
120 114 
 importFrom(doParallel,registerDoParallel)
121 115 
 importFrom(enrichR,enrichr)
122 116 
 importFrom(enrichR,listEnrichrDbs)
123 
-importFrom(ggdendro,dendro_data)
124 
-importFrom(ggdendro,ggdendrogram)
125 117 
 importFrom(ggrepel,geom_text_repel)
126 118 
 importFrom(grDevices,colorRampPalette)
127 119 
 importFrom(grDevices,colors)
... ... 
@@ -136,12 +128,8 @@ importFrom(gtable,gtable_height)
136 128 
 importFrom(gtable,gtable_width)
137 129 
 importFrom(matrixStats,logSumExp)
138 130 
 importFrom(methods,.hasSlot)
139 
-importFrom(methods,hasArg)
140 131 
 importFrom(methods,is)
141 132 
 importFrom(methods,new)
142 
-importFrom(pROC,auc)
143 
-importFrom(pROC,coords)
144 
-importFrom(pROC,roc)
145 133 
 importFrom(plyr,.)
146 134 
 importFrom(plyr,mapvalues)
147 135 
 importFrom(reshape2,melt)
Browse code

updated for marker tree functions

Ahmed Youssef authored on 31/01/2020 05:33:47 • GitHub committed on 31/01/2020 05:33:47
Showing 1 changed files
NAMESPACE
History View file @ c01b818a
... ... 
@@ -25,9 +25,8 @@ export(distinctColors)
25 25 
 export(factorizeMatrix)
26 26 
 export(featureModuleLookup)
27 27 
 export(featureModuleTable)
28 
-export(findMarkers)
28 
+export(findMarkersTree)
29 29 
 export(geneSetEnrich)
30 
-export(getDecisions)
31 30 
 export(logLikelihood)
32 31 
 export(logLikelihoodHistory)
33 32 
 export(logLikelihoodcelda_C)
... ... 
@@ -48,6 +47,7 @@ export(plotGridSearchPerplexitycelda_C)
48 47 
 export(plotGridSearchPerplexitycelda_CG)
49 48 
 export(plotGridSearchPerplexitycelda_G)
50 49 
 export(plotHeatmap)
50 
+export(plotMarkerHeatmap)
51 51 
 export(recodeClusterY)
52 52 
 export(recodeClusterZ)
53 53 
 export(recursiveSplitCell)
... ... 
@@ -90,6 +90,7 @@ import(Rcpp)
90 90 
 import(RcppEigen)
91 91 
 import(SummarizedExperiment)
92 92 
 import(data.table, except = c(melt, shift))
93 
+import(dbscan)
93 94 
 import(foreach)
94 95 
 import(ggplot2)
95 96 
 import(grDevices)
... ... 
@@ -97,8 +98,10 @@ import(graphics)
97 98 
 import(grid)
98 99 
 import(gridExtra, except = c(combine))
99 100 
 import(magrittr)
101 
+import(pROC)
100 102 
 import(stats, except = c(start, end))
101 103 
 import(uwot)
104 
+import(withr)
102 105 
 importFrom(MAST,FromMatrix)
103 106 
 importFrom(MAST,summary)
104 107 
 importFrom(MAST,zlm)
Browse code

Updated decontX documentation

Joshua D. Campbell authored on 07/01/2020 21:45:50
Showing 1 changed files
NAMESPACE
History