mikejiang authored on 04/08/2021 04:04:36
| ... | ... |
@@ -6,8 +6,6 @@ S3method(extend,ellipsoidGate) |
| 6 | 6 |
S3method(extend,polygonGate) |
| 7 | 7 |
S3method(extend,rectangleGate) |
| 8 | 8 |
S3method(print,cytobank_experiment) |
| 9 |
-export(CytoML.par.get) |
|
| 10 |
-export(CytoML.par.set) |
|
| 11 | 9 |
export(GatingSet2cytobank) |
| 12 | 10 |
export(GatingSet2flowJo) |
| 13 | 11 |
export(ce_get_channels) |
| ... | ... |
@@ -84,11 +82,10 @@ importFrom(XML,xmlTreeParse) |
| 84 | 82 |
importFrom(XML,xmlValue) |
| 85 | 83 |
importFrom(XML,xpathApply) |
| 86 | 84 |
importFrom(XML,xpathSApply) |
| 87 |
-importFrom(base64enc,base64decode) |
|
| 88 |
-importFrom(base64enc,base64encode) |
|
| 89 | 85 |
importFrom(cytolib,cytolib_LdFlags) |
| 90 | 86 |
importFrom(dplyr,"%>%") |
| 91 | 87 |
importFrom(dplyr,arrange) |
| 88 |
+importFrom(dplyr,bind_rows) |
|
| 92 | 89 |
importFrom(dplyr,count) |
| 93 | 90 |
importFrom(dplyr,enquo) |
| 94 | 91 |
importFrom(dplyr,filter) |
| ... | ... |
@@ -189,6 +186,8 @@ importFrom(graph,removeNode) |
| 189 | 186 |
importFrom(graphics,abline) |
| 190 | 187 |
importFrom(graphics,polygon) |
| 191 | 188 |
importFrom(graphics,text) |
| 189 |
+importFrom(jsonlite,base64_dec) |
|
| 190 |
+importFrom(jsonlite,base64_enc) |
|
| 192 | 191 |
importFrom(jsonlite,fromJSON) |
| 193 | 192 |
importFrom(jsonlite,toJSON) |
| 194 | 193 |
importFrom(methods,as) |
| ... | ... |
@@ -202,9 +201,5 @@ importFrom(tibble,tibble) |
| 202 | 201 |
importFrom(utils,localeToCharset) |
| 203 | 202 |
importFrom(utils,menu) |
| 204 | 203 |
importFrom(utils,packageVersion) |
| 205 |
-importFrom(xml2,read_xml) |
|
| 206 |
-importFrom(xml2,write_xml) |
|
| 207 |
-importFrom(xml2,xml_add_sibling) |
|
| 208 |
-importFrom(xml2,xml_comment) |
|
| 209 | 204 |
importFrom(yaml,read_yaml) |
| 210 | 205 |
useDynLib(CytoML,.registration = TRUE) |
mikejiang authored on 20/07/2021 20:58:09
| ... | ... |
@@ -198,8 +198,6 @@ importFrom(methods,new) |
| 198 | 198 |
importFrom(methods,selectMethod) |
| 199 | 199 |
importFrom(methods,show) |
| 200 | 200 |
importFrom(methods,slot) |
| 201 |
-importFrom(plyr,ldply) |
|
| 202 |
-importFrom(plyr,name_rows) |
|
| 203 | 201 |
importFrom(tibble,tibble) |
| 204 | 202 |
importFrom(utils,localeToCharset) |
| 205 | 203 |
importFrom(utils,menu) |
mikejiang authored on 19/07/2021 23:50:37
| ... | ... |
@@ -62,7 +62,6 @@ importClassesFrom(methods,missing) |
| 62 | 62 |
importClassesFrom(methods,numeric) |
| 63 | 63 |
importClassesFrom(methods,oldClass) |
| 64 | 64 |
importFrom(RBGL,tsort) |
| 65 |
-importFrom(RcppParallel,RcppParallelLibs) |
|
| 66 | 65 |
importFrom(Rgraphviz,layoutGraph) |
| 67 | 66 |
importFrom(Rgraphviz,renderGraph) |
| 68 | 67 |
importFrom(XML,"xmlAttrs<-") |
mikejiang authored on 07/12/2020 04:32:54
| ... | ... |
@@ -10,7 +10,9 @@ export(CytoML.par.get) |
| 10 | 10 |
export(CytoML.par.set) |
| 11 | 11 |
export(GatingSet2cytobank) |
| 12 | 12 |
export(GatingSet2flowJo) |
| 13 |
+export(ce_get_channels) |
|
| 13 | 14 |
export(ce_get_compensations) |
| 15 |
+export(ce_get_markers) |
|
| 14 | 16 |
export(ce_get_panels) |
| 15 | 17 |
export(ce_get_samples) |
| 16 | 18 |
export(ce_get_transformations) |
mikejiang authored on 13/10/2020 23:21:04
| ... | ... |
@@ -87,10 +87,13 @@ importFrom(base64enc,base64decode) |
| 87 | 87 |
importFrom(base64enc,base64encode) |
| 88 | 88 |
importFrom(cytolib,cytolib_LdFlags) |
| 89 | 89 |
importFrom(dplyr,"%>%") |
| 90 |
+importFrom(dplyr,arrange) |
|
| 90 | 91 |
importFrom(dplyr,count) |
| 91 | 92 |
importFrom(dplyr,enquo) |
| 92 | 93 |
importFrom(dplyr,filter) |
| 94 |
+importFrom(dplyr,group_by) |
|
| 93 | 95 |
importFrom(dplyr,rename) |
| 96 |
+importFrom(dplyr,select) |
|
| 94 | 97 |
importFrom(flowCore,"colnames<-") |
| 95 | 98 |
importFrom(flowCore,"identifier<-") |
| 96 | 99 |
importFrom(flowCore,"parameters<-") |
Jacob Wagner authored on 09/07/2020 20:08:20
| ... | ... |
@@ -122,6 +122,7 @@ importFrom(flowWorkspace,asinhtGml2_trans) |
| 122 | 122 |
importFrom(flowWorkspace,cf_write_disk) |
| 123 | 123 |
importFrom(flowWorkspace,cs_load_meta) |
| 124 | 124 |
importFrom(flowWorkspace,cs_lock) |
| 125 |
+importFrom(flowWorkspace,cs_set_cytoframe) |
|
| 125 | 126 |
importFrom(flowWorkspace,cs_swap_colnames) |
| 126 | 127 |
importFrom(flowWorkspace,cs_unlock) |
| 127 | 128 |
importFrom(flowWorkspace,cytoset) |
mikejiang authored on 01/07/2020 18:55:09
| ... | ... |
@@ -120,13 +120,11 @@ importFrom(flowWorkspace,GatingSet) |
| 120 | 120 |
importFrom(flowWorkspace,asinh_Gml2) |
| 121 | 121 |
importFrom(flowWorkspace,asinhtGml2_trans) |
| 122 | 122 |
importFrom(flowWorkspace,cf_write_disk) |
| 123 |
-importFrom(flowWorkspace,compute_timestep) |
|
| 124 | 123 |
importFrom(flowWorkspace,cs_load_meta) |
| 125 | 124 |
importFrom(flowWorkspace,cs_lock) |
| 126 | 125 |
importFrom(flowWorkspace,cs_swap_colnames) |
| 127 | 126 |
importFrom(flowWorkspace,cs_unlock) |
| 128 | 127 |
importFrom(flowWorkspace,cytoset) |
| 129 |
-importFrom(flowWorkspace,fix_channel_slash) |
|
| 130 | 128 |
importFrom(flowWorkspace,flow_trans) |
| 131 | 129 |
importFrom(flowWorkspace,getChildren) |
| 132 | 130 |
importFrom(flowWorkspace,getCompensationMatrices) |
mikejiang authored on 19/06/2020 04:20:14
| ... | ... |
@@ -119,7 +119,7 @@ importFrom(flowWorkspace,"pData<-") |
| 119 | 119 |
importFrom(flowWorkspace,GatingSet) |
| 120 | 120 |
importFrom(flowWorkspace,asinh_Gml2) |
| 121 | 121 |
importFrom(flowWorkspace,asinhtGml2_trans) |
| 122 |
-importFrom(flowWorkspace,cf_write_h5) |
|
| 122 |
+importFrom(flowWorkspace,cf_write_disk) |
|
| 123 | 123 |
importFrom(flowWorkspace,compute_timestep) |
| 124 | 124 |
importFrom(flowWorkspace,cs_load_meta) |
| 125 | 125 |
importFrom(flowWorkspace,cs_lock) |
| ... | ... |
@@ -135,6 +135,7 @@ importFrom(flowWorkspace,getNodes) |
| 135 | 135 |
importFrom(flowWorkspace,getParent) |
| 136 | 136 |
importFrom(flowWorkspace,getTransformations) |
| 137 | 137 |
importFrom(flowWorkspace,get_cytoframe_from_cs) |
| 138 |
+importFrom(flowWorkspace,get_default_backend) |
|
| 138 | 139 |
importFrom(flowWorkspace,gh_pop_compare_stats) |
| 139 | 140 |
importFrom(flowWorkspace,gh_pop_get_data) |
| 140 | 141 |
importFrom(flowWorkspace,gh_pop_is_hidden) |
| ... | ... |
@@ -151,7 +152,7 @@ importFrom(flowWorkspace,gs_pop_get_parent) |
| 151 | 152 |
importFrom(flowWorkspace,gs_pop_set_name) |
| 152 | 153 |
importFrom(flowWorkspace,gs_split_by_tree) |
| 153 | 154 |
importFrom(flowWorkspace,gs_update_channels) |
| 154 |
-importFrom(flowWorkspace,load_cytoframe_from_h5) |
|
| 155 |
+importFrom(flowWorkspace,load_cytoframe) |
|
| 155 | 156 |
importFrom(flowWorkspace,load_cytoset_from_fcs) |
| 156 | 157 |
importFrom(flowWorkspace,load_gs) |
| 157 | 158 |
importFrom(flowWorkspace,logicleGml2_trans) |
mikejiang authored on 02/06/2020 18:47:17
| ... | ... |
@@ -125,6 +125,7 @@ importFrom(flowWorkspace,cs_load_meta) |
| 125 | 125 |
importFrom(flowWorkspace,cs_lock) |
| 126 | 126 |
importFrom(flowWorkspace,cs_swap_colnames) |
| 127 | 127 |
importFrom(flowWorkspace,cs_unlock) |
| 128 |
+importFrom(flowWorkspace,cytoset) |
|
| 128 | 129 |
importFrom(flowWorkspace,fix_channel_slash) |
| 129 | 130 |
importFrom(flowWorkspace,flow_trans) |
| 130 | 131 |
importFrom(flowWorkspace,getChildren) |
mikejiang authored on 30/05/2020 19:30:43
| ... | ... |
@@ -201,7 +201,6 @@ importFrom(utils,menu) |
| 201 | 201 |
importFrom(utils,packageVersion) |
| 202 | 202 |
importFrom(xml2,read_xml) |
| 203 | 203 |
importFrom(xml2,write_xml) |
| 204 |
-importFrom(xml2,xml_add_child) |
|
| 205 | 204 |
importFrom(xml2,xml_add_sibling) |
| 206 | 205 |
importFrom(xml2,xml_comment) |
| 207 | 206 |
importFrom(yaml,read_yaml) |
mikejiang authored on 27/05/2020 23:05:57
| ... | ... |
@@ -199,5 +199,10 @@ importFrom(tibble,tibble) |
| 199 | 199 |
importFrom(utils,localeToCharset) |
| 200 | 200 |
importFrom(utils,menu) |
| 201 | 201 |
importFrom(utils,packageVersion) |
| 202 |
+importFrom(xml2,read_xml) |
|
| 203 |
+importFrom(xml2,write_xml) |
|
| 204 |
+importFrom(xml2,xml_add_child) |
|
| 205 |
+importFrom(xml2,xml_add_sibling) |
|
| 206 |
+importFrom(xml2,xml_comment) |
|
| 202 | 207 |
importFrom(yaml,read_yaml) |
| 203 | 208 |
useDynLib(CytoML,.registration = TRUE) |
Jacob Wagner authored on 26/05/2020 22:33:11
mikejiang authored on 20/04/2020 22:13:03
| ... | ... |
@@ -25,7 +25,6 @@ export(fj_ws_get_keywords) |
| 25 | 25 |
export(fj_ws_get_sample_groups) |
| 26 | 26 |
export(fj_ws_get_samples) |
| 27 | 27 |
export(flowjo_to_gatingset) |
| 28 |
-export(gating_graphGML) |
|
| 29 | 28 |
export(gatingset_to_cytobank) |
| 30 | 29 |
export(gatingset_to_flowjo) |
| 31 | 30 |
export(getKeywords) |
| ... | ... |
@@ -46,7 +45,6 @@ exportMethods(parseWorkspace) |
| 46 | 45 |
exportMethods(sampleNames) |
| 47 | 46 |
exportMethods(show) |
| 48 | 47 |
import(data.table) |
| 49 |
-import(flowCore) |
|
| 50 | 48 |
importClassesFrom(Biobase,AssayData) |
| 51 | 49 |
importClassesFrom(graph,graph) |
| 52 | 50 |
importClassesFrom(graph,graphBase) |
| ... | ... |
@@ -103,6 +101,7 @@ importFrom(flowCore,compensation) |
| 103 | 101 |
importFrom(flowCore,ellipsoidGate) |
| 104 | 102 |
importFrom(flowCore,eval) |
| 105 | 103 |
importFrom(flowCore,identifier) |
| 104 |
+importFrom(flowCore,keyword) |
|
| 106 | 105 |
importFrom(flowCore,logicleTransform) |
| 107 | 106 |
importFrom(flowCore,logicletGml2) |
| 108 | 107 |
importFrom(flowCore,logtGml2) |
mikejiang authored on 20/04/2020 21:34:04
mikejiang authored on 11/03/2020 00:28:02
| ... | ... |
@@ -152,6 +152,7 @@ importFrom(flowWorkspace,gs_pop_set_name) |
| 152 | 152 |
importFrom(flowWorkspace,gs_split_by_tree) |
| 153 | 153 |
importFrom(flowWorkspace,gs_update_channels) |
| 154 | 154 |
importFrom(flowWorkspace,load_cytoframe_from_h5) |
| 155 |
+importFrom(flowWorkspace,load_cytoset_from_fcs) |
|
| 155 | 156 |
importFrom(flowWorkspace,load_gs) |
| 156 | 157 |
importFrom(flowWorkspace,logicleGml2_trans) |
| 157 | 158 |
importFrom(flowWorkspace,logicle_trans) |
| ... | ... |
@@ -193,7 +194,6 @@ importFrom(methods,new) |
| 193 | 194 |
importFrom(methods,selectMethod) |
| 194 | 195 |
importFrom(methods,show) |
| 195 | 196 |
importFrom(methods,slot) |
| 196 |
-importFrom(ncdfFlow,read.ncdfFlowSet) |
|
| 197 | 197 |
importFrom(plyr,ldply) |
| 198 | 198 |
importFrom(plyr,name_rows) |
| 199 | 199 |
importFrom(tibble,tibble) |
Jacob Wagner authored on 22/01/2020 19:09:37
| ... | ... |
@@ -157,6 +157,7 @@ importFrom(flowWorkspace,logicleGml2_trans) |
| 157 | 157 |
importFrom(flowWorkspace,logicle_trans) |
| 158 | 158 |
importFrom(flowWorkspace,logtGml2_trans) |
| 159 | 159 |
importFrom(flowWorkspace,markernames) |
| 160 |
+importFrom(flowWorkspace,merge_list_to_gs) |
|
| 160 | 161 |
importFrom(flowWorkspace,openWorkspace) |
| 161 | 162 |
importFrom(flowWorkspace,pData) |
| 162 | 163 |
importFrom(flowWorkspace,pop_add) |
Jacob Wagner authored on 22/01/2020 19:07:39
| ... | ... |
@@ -118,7 +118,6 @@ importFrom(flowCore,unitytransform) |
| 118 | 118 |
importFrom(flowWorkspace,"markernames<-") |
| 119 | 119 |
importFrom(flowWorkspace,"pData<-") |
| 120 | 120 |
importFrom(flowWorkspace,GatingSet) |
| 121 |
-importFrom(flowWorkspace,GatingSetList) |
|
| 122 | 121 |
importFrom(flowWorkspace,asinh_Gml2) |
| 123 | 122 |
importFrom(flowWorkspace,asinhtGml2_trans) |
| 124 | 123 |
importFrom(flowWorkspace,cf_write_h5) |
| ... | ... |
@@ -152,7 +151,6 @@ importFrom(flowWorkspace,gs_pop_get_parent) |
| 152 | 151 |
importFrom(flowWorkspace,gs_pop_set_name) |
| 153 | 152 |
importFrom(flowWorkspace,gs_split_by_tree) |
| 154 | 153 |
importFrom(flowWorkspace,gs_update_channels) |
| 155 |
-importFrom(flowWorkspace,gslist_to_gs) |
|
| 156 | 154 |
importFrom(flowWorkspace,load_cytoframe_from_h5) |
| 157 | 155 |
importFrom(flowWorkspace,load_gs) |
| 158 | 156 |
importFrom(flowWorkspace,logicleGml2_trans) |
mikejiang authored on 21/11/2019 21:03:38
mikejiang authored on 21/11/2019 19:50:16
Jacob Wagner authored on 21/11/2019 18:32:00
mikejiang authored on 20/11/2019 23:54:48
| ... | ... |
@@ -25,6 +25,7 @@ export(fj_ws_get_keywords) |
| 25 | 25 |
export(fj_ws_get_sample_groups) |
| 26 | 26 |
export(fj_ws_get_samples) |
| 27 | 27 |
export(flowjo_to_gatingset) |
| 28 |
+export(gating_graphGML) |
|
| 28 | 29 |
export(gatingset_to_cytobank) |
| 29 | 30 |
export(gatingset_to_flowjo) |
| 30 | 31 |
export(getKeywords) |
| ... | ... |
@@ -200,7 +201,6 @@ importFrom(methods,selectMethod) |
| 200 | 201 |
importFrom(methods,show) |
| 201 | 202 |
importFrom(methods,slot) |
| 202 | 203 |
importFrom(ncdfFlow,read.ncdfFlowSet) |
| 203 |
-importFrom(openCyto,gating) |
|
| 204 | 204 |
importFrom(plyr,ldply) |
| 205 | 205 |
importFrom(plyr,name_rows) |
| 206 | 206 |
importFrom(tibble,tibble) |
Jacob Wagner authored on 01/11/2019 23:42:20
| ... | ... |
@@ -10,7 +10,7 @@ export(CytoML.par.get) |
| 10 | 10 |
export(CytoML.par.set) |
| 11 | 11 |
export(GatingSet2cytobank) |
| 12 | 12 |
export(GatingSet2flowJo) |
| 13 |
-export(ce_get_cmpensations) |
|
| 13 |
+export(ce_get_compensations) |
|
| 14 | 14 |
export(ce_get_panels) |
| 15 | 15 |
export(ce_get_samples) |
| 16 | 16 |
export(ce_get_transformations) |
Jacob Wagner authored on 01/11/2019 23:42:20
| ... | ... |
@@ -10,7 +10,7 @@ export(CytoML.par.get) |
| 10 | 10 |
export(CytoML.par.set) |
| 11 | 11 |
export(GatingSet2cytobank) |
| 12 | 12 |
export(GatingSet2flowJo) |
| 13 |
-export(ce_get_cmpensations) |
|
| 13 |
+export(ce_get_compensations) |
|
| 14 | 14 |
export(ce_get_panels) |
| 15 | 15 |
export(ce_get_samples) |
| 16 | 16 |
export(ce_get_transformations) |
mikejiang authored on 01/11/2019 17:38:22
| ... | ... |
@@ -11,6 +11,8 @@ export(CytoML.par.set) |
| 11 | 11 |
export(GatingSet2cytobank) |
| 12 | 12 |
export(GatingSet2flowJo) |
| 13 | 13 |
export(ce_get_cmpensations) |
| 14 |
+export(ce_get_panels) |
|
| 15 |
+export(ce_get_samples) |
|
| 14 | 16 |
export(ce_get_transformations) |
| 15 | 17 |
export(cytobank2GatingSet) |
| 16 | 18 |
export(cytobankExperiment) |
| ... | ... |
@@ -86,6 +88,10 @@ importFrom(XML,xpathSApply) |
| 86 | 88 |
importFrom(base64enc,base64decode) |
| 87 | 89 |
importFrom(base64enc,base64encode) |
| 88 | 90 |
importFrom(cytolib,cytolib_LdFlags) |
| 91 |
+importFrom(dplyr,"%>%") |
|
| 92 |
+importFrom(dplyr,count) |
|
| 93 |
+importFrom(dplyr,filter) |
|
| 94 |
+importFrom(dplyr,rename) |
|
| 89 | 95 |
importFrom(flowCore,"colnames<-") |
| 90 | 96 |
importFrom(flowCore,"identifier<-") |
| 91 | 97 |
importFrom(flowCore,"parameters<-") |
| ... | ... |
@@ -197,6 +203,7 @@ importFrom(ncdfFlow,read.ncdfFlowSet) |
| 197 | 203 |
importFrom(openCyto,gating) |
| 198 | 204 |
importFrom(plyr,ldply) |
| 199 | 205 |
importFrom(plyr,name_rows) |
| 206 |
+importFrom(tibble,tibble) |
|
| 200 | 207 |
importFrom(utils,localeToCharset) |
| 201 | 208 |
importFrom(utils,menu) |
| 202 | 209 |
importFrom(utils,packageVersion) |
mikejiang authored on 30/10/2019 23:41:53
| ... | ... |
@@ -11,6 +11,8 @@ export(CytoML.par.set) |
| 11 | 11 |
export(GatingSet2cytobank) |
| 12 | 12 |
export(GatingSet2flowJo) |
| 13 | 13 |
export(ce_get_cmpensations) |
| 14 |
+export(ce_get_panels) |
|
| 15 |
+export(ce_get_samples) |
|
| 14 | 16 |
export(ce_get_transformations) |
| 15 | 17 |
export(closeWorkspace) |
| 16 | 18 |
export(cytobank2GatingSet) |
| ... | ... |
@@ -89,8 +91,11 @@ importFrom(XML,xpathSApply) |
| 89 | 91 |
importFrom(base64enc,base64decode) |
| 90 | 92 |
importFrom(base64enc,base64encode) |
| 91 | 93 |
importFrom(dplyr,"%>%") |
| 94 |
+importFrom(dplyr,count) |
|
| 92 | 95 |
importFrom(dplyr,do) |
| 96 |
+importFrom(dplyr,filter) |
|
| 93 | 97 |
importFrom(dplyr,group_by) |
| 98 |
+importFrom(dplyr,rename) |
|
| 94 | 99 |
importFrom(flowCore,"colnames<-") |
| 95 | 100 |
importFrom(flowCore,"identifier<-") |
| 96 | 101 |
importFrom(flowCore,"parameters<-") |
| ... | ... |
@@ -195,6 +200,7 @@ importFrom(openCyto,gating) |
| 195 | 200 |
importFrom(plyr,ldply) |
| 196 | 201 |
importFrom(plyr,name_rows) |
| 197 | 202 |
importFrom(stats,na.omit) |
| 203 |
+importFrom(tibble,tibble) |
|
| 198 | 204 |
importFrom(utils,localeToCharset) |
| 199 | 205 |
importFrom(utils,menu) |
| 200 | 206 |
importFrom(utils,packageVersion) |
mikejiang authored on 26/09/2019 21:55:13
| ... | ... |
@@ -96,7 +96,6 @@ importFrom(flowCore,compensatedParameter) |
| 96 | 96 |
importFrom(flowCore,compensation) |
| 97 | 97 |
importFrom(flowCore,ellipsoidGate) |
| 98 | 98 |
importFrom(flowCore,eval) |
| 99 |
-importFrom(flowCore,exprs) |
|
| 100 | 99 |
importFrom(flowCore,identifier) |
| 101 | 100 |
importFrom(flowCore,logicleTransform) |
| 102 | 101 |
importFrom(flowCore,logicletGml2) |
| ... | ... |
@@ -121,8 +120,6 @@ importFrom(flowWorkspace,cs_load_meta) |
| 121 | 120 |
importFrom(flowWorkspace,cs_lock) |
| 122 | 121 |
importFrom(flowWorkspace,cs_swap_colnames) |
| 123 | 122 |
importFrom(flowWorkspace,cs_unlock) |
| 124 |
-importFrom(flowWorkspace,extract_cluster_pop_name_from_node) |
|
| 125 |
-importFrom(flowWorkspace,filterObject) |
|
| 126 | 123 |
importFrom(flowWorkspace,fix_channel_slash) |
| 127 | 124 |
importFrom(flowWorkspace,flow_trans) |
| 128 | 125 |
importFrom(flowWorkspace,getChildren) |
| ... | ... |
@@ -132,11 +129,8 @@ importFrom(flowWorkspace,getNodes) |
| 132 | 129 |
importFrom(flowWorkspace,getParent) |
| 133 | 130 |
importFrom(flowWorkspace,getTransformations) |
| 134 | 131 |
importFrom(flowWorkspace,get_cytoframe_from_cs) |
| 135 |
-importFrom(flowWorkspace,gh_get_cluster_labels) |
|
| 136 | 132 |
importFrom(flowWorkspace,gh_pop_compare_stats) |
| 137 |
-importFrom(flowWorkspace,gh_pop_get_cluster_name) |
|
| 138 | 133 |
importFrom(flowWorkspace,gh_pop_get_data) |
| 139 |
-importFrom(flowWorkspace,gh_pop_get_stats) |
|
| 140 | 134 |
importFrom(flowWorkspace,gh_pop_is_hidden) |
| 141 | 135 |
importFrom(flowWorkspace,gh_pop_is_negated) |
| 142 | 136 |
importFrom(flowWorkspace,gh_pop_set_xml_count) |
| ... | ... |
@@ -152,7 +146,6 @@ importFrom(flowWorkspace,gs_pop_set_name) |
| 152 | 146 |
importFrom(flowWorkspace,gs_split_by_tree) |
| 153 | 147 |
importFrom(flowWorkspace,gs_update_channels) |
| 154 | 148 |
importFrom(flowWorkspace,gslist_to_gs) |
| 155 |
-importFrom(flowWorkspace,keyword) |
|
| 156 | 149 |
importFrom(flowWorkspace,load_cytoframe_from_h5) |
| 157 | 150 |
importFrom(flowWorkspace,load_gs) |
| 158 | 151 |
importFrom(flowWorkspace,logicleGml2_trans) |
mikejiang authored on 25/09/2019 21:50:20
| ... | ... |
@@ -85,6 +85,7 @@ importFrom(XML,xpathApply) |
| 85 | 85 |
importFrom(XML,xpathSApply) |
| 86 | 86 |
importFrom(base64enc,base64decode) |
| 87 | 87 |
importFrom(base64enc,base64encode) |
| 88 |
+importFrom(cytolib,cytolib_LdFlags) |
|
| 88 | 89 |
importFrom(flowCore,"colnames<-") |
| 89 | 90 |
importFrom(flowCore,"identifier<-") |
| 90 | 91 |
importFrom(flowCore,"parameters<-") |
mikejiang authored on 25/09/2019 21:50:20
| ... | ... |
@@ -85,6 +85,7 @@ importFrom(XML,xpathApply) |
| 85 | 85 |
importFrom(XML,xpathSApply) |
| 86 | 86 |
importFrom(base64enc,base64decode) |
| 87 | 87 |
importFrom(base64enc,base64encode) |
| 88 |
+importFrom(cytolib,cytolib_LdFlags) |
|
| 88 | 89 |
importFrom(flowCore,"colnames<-") |
| 89 | 90 |
importFrom(flowCore,"identifier<-") |
| 90 | 91 |
importFrom(flowCore,"parameters<-") |
Jacob Wagner authored on 16/08/2019 19:16:40
| ... | ... |
@@ -157,6 +157,7 @@ importFrom(flowWorkspace,logicle_trans) |
| 157 | 157 |
importFrom(flowWorkspace,logtGml2_trans) |
| 158 | 158 |
importFrom(flowWorkspace,markernames) |
| 159 | 159 |
importFrom(flowWorkspace,pData) |
| 160 |
+importFrom(flowWorkspace,pop_add) |
|
| 160 | 161 |
importFrom(flowWorkspace,recompute) |
| 161 | 162 |
importFrom(flowWorkspace,sampleNames) |
| 162 | 163 |
importFrom(flowWorkspace,save_gs) |
mikejiang authored on 12/07/2019 22:17:31
mikejiang authored on 07/06/2019 17:44:52
| ... | ... |
@@ -150,6 +150,7 @@ importFrom(flowWorkspace,gs_pop_get_parent) |
| 150 | 150 |
importFrom(flowWorkspace,gs_pop_set_name) |
| 151 | 151 |
importFrom(flowWorkspace,gs_split_by_tree) |
| 152 | 152 |
importFrom(flowWorkspace,gs_update_channels) |
| 153 |
+importFrom(flowWorkspace,gslist_to_gs) |
|
| 153 | 154 |
importFrom(flowWorkspace,keyword) |
| 154 | 155 |
importFrom(flowWorkspace,load_cytoframe_from_h5) |
| 155 | 156 |
importFrom(flowWorkspace,load_gs) |
| ... | ... |
@@ -159,7 +160,6 @@ importFrom(flowWorkspace,logtGml2_trans) |
| 159 | 160 |
importFrom(flowWorkspace,markernames) |
| 160 | 161 |
importFrom(flowWorkspace,openWorkspace) |
| 161 | 162 |
importFrom(flowWorkspace,pData) |
| 162 |
-importFrom(flowWorkspace,rbind2) |
|
| 163 | 163 |
importFrom(flowWorkspace,recompute) |
| 164 | 164 |
importFrom(flowWorkspace,sampleNames) |
| 165 | 165 |
importFrom(flowWorkspace,save_gs) |
mikejiang authored on 20/05/2019 18:34:26
Jacob Wagner authored on 14/05/2019 18:58:52
| ... | ... |
@@ -113,6 +113,8 @@ importFrom(flowCore,read.FCSheader) |
| 113 | 113 |
importFrom(flowCore,rectangleGate) |
| 114 | 114 |
importFrom(flowCore,spillover) |
| 115 | 115 |
importFrom(flowCore,transformList) |
| 116 |
+importFrom(flowCore,transformReference) |
|
| 117 |
+importFrom(flowCore,unitytransform) |
|
| 116 | 118 |
importFrom(flowWorkspace,"markernames<-") |
| 117 | 119 |
importFrom(flowWorkspace,"pData<-") |
| 118 | 120 |
importFrom(flowWorkspace,GatingSet) |
Jacob Wagner authored on 09/05/2019 18:30:24
Jacob Wagner authored on 07/05/2019 18:59:17
Jacob Wagner authored on 06/05/2019 19:26:38
| ... | ... |
@@ -111,8 +111,6 @@ importFrom(flowCore,read.FCSheader) |
| 111 | 111 |
importFrom(flowCore,rectangleGate) |
| 112 | 112 |
importFrom(flowCore,spillover) |
| 113 | 113 |
importFrom(flowCore,transformList) |
| 114 |
-importFrom(flowUtils,read.gatingML) |
|
| 115 |
-importFrom(flowUtils,write.gatingML) |
|
| 116 | 114 |
importFrom(flowWorkspace,"markernames<-") |
| 117 | 115 |
importFrom(flowWorkspace,"pData<-") |
| 118 | 116 |
importFrom(flowWorkspace,GatingSet) |
mikejiang authored on 30/04/2019 23:49:54
mikejiang authored on 30/04/2019 23:43:41
| ... | ... |
@@ -113,6 +113,7 @@ importFrom(flowCore,logtGml2) |
| 113 | 113 |
importFrom(flowCore,parameters) |
| 114 | 114 |
importFrom(flowCore,polygonGate) |
| 115 | 115 |
importFrom(flowCore,read.FCS) |
| 116 |
+importFrom(flowCore,read.FCSheader) |
|
| 116 | 117 |
importFrom(flowCore,rectangleGate) |
| 117 | 118 |
importFrom(flowCore,spillover) |
| 118 | 119 |
importFrom(flowCore,transformList) |
mikejiang authored on 22/04/2019 18:02:18
| ... | ... |
@@ -116,7 +116,6 @@ importFrom(flowWorkspace,"markernames<-") |
| 116 | 116 |
importFrom(flowWorkspace,"pData<-") |
| 117 | 117 |
importFrom(flowWorkspace,GatingSet) |
| 118 | 118 |
importFrom(flowWorkspace,GatingSetList) |
| 119 |
-importFrom(flowWorkspace,add) |
|
| 120 | 119 |
importFrom(flowWorkspace,asinh_Gml2) |
| 121 | 120 |
importFrom(flowWorkspace,asinhtGml2_trans) |
| 122 | 121 |
importFrom(flowWorkspace,compute_timestep) |
| ... | ... |
@@ -140,6 +139,10 @@ importFrom(flowWorkspace,gh_pop_is_negated) |
| 140 | 139 |
importFrom(flowWorkspace,gh_pop_set_xml_count) |
| 141 | 140 |
importFrom(flowWorkspace,gs_clone) |
| 142 | 141 |
importFrom(flowWorkspace,gs_get_compensation_internal) |
| 142 |
+importFrom(flowWorkspace,gs_pop_add) |
|
| 143 |
+importFrom(flowWorkspace,gs_pop_get_children) |
|
| 144 |
+importFrom(flowWorkspace,gs_pop_get_count_fast) |
|
| 145 |
+importFrom(flowWorkspace,gs_pop_get_data) |
|
| 143 | 146 |
importFrom(flowWorkspace,gs_pop_get_parent) |
| 144 | 147 |
importFrom(flowWorkspace,gs_pop_set_name) |
| 145 | 148 |
importFrom(flowWorkspace,gs_split_by_tree) |
mikejiang authored on 19/04/2019 22:36:43
| ... | ... |
@@ -137,6 +137,7 @@ importFrom(flowWorkspace,gh_pop_get_data) |
| 137 | 137 |
importFrom(flowWorkspace,gh_pop_get_stats) |
| 138 | 138 |
importFrom(flowWorkspace,gh_pop_is_hidden) |
| 139 | 139 |
importFrom(flowWorkspace,gh_pop_is_negated) |
| 140 |
+importFrom(flowWorkspace,gh_pop_set_xml_count) |
|
| 140 | 141 |
importFrom(flowWorkspace,gs_clone) |
| 141 | 142 |
importFrom(flowWorkspace,gs_get_compensation_internal) |
| 142 | 143 |
importFrom(flowWorkspace,gs_pop_get_parent) |
| ... | ... |
@@ -153,7 +154,6 @@ importFrom(flowWorkspace,pData) |
| 153 | 154 |
importFrom(flowWorkspace,recompute) |
| 154 | 155 |
importFrom(flowWorkspace,sampleNames) |
| 155 | 156 |
importFrom(flowWorkspace,save_gs) |
| 156 |
-importFrom(flowWorkspace,set.count.xml) |
|
| 157 | 157 |
importFrom(flowWorkspace,show) |
| 158 | 158 |
importFrom(flowWorkspace,swap_data_cols) |
| 159 | 159 |
importFrom(flowWorkspace,transform) |
mikejiang authored on 18/04/2019 22:53:13
| ... | ... |
@@ -130,18 +130,19 @@ importFrom(flowWorkspace,getGate) |
| 130 | 130 |
importFrom(flowWorkspace,getNodes) |
| 131 | 131 |
importFrom(flowWorkspace,getParent) |
| 132 | 132 |
importFrom(flowWorkspace,getTransformations) |
| 133 |
-importFrom(flowWorkspace,gh_check_cluster_node) |
|
| 134 | 133 |
importFrom(flowWorkspace,gh_get_cluster_labels) |
| 135 |
-importFrom(flowWorkspace,gh_get_count) |
|
| 136 |
-importFrom(flowWorkspace,gh_get_data) |
|
| 137 |
-importFrom(flowWorkspace,gh_get_pop_stats) |
|
| 138 |
-importFrom(flowWorkspace,gh_is_hidden) |
|
| 139 |
-importFrom(flowWorkspace,gh_is_negated) |
|
| 140 |
-importFrom(flowWorkspace,groupByTree) |
|
| 134 |
+importFrom(flowWorkspace,gh_pop_compare_stats) |
|
| 135 |
+importFrom(flowWorkspace,gh_pop_get_cluster_name) |
|
| 136 |
+importFrom(flowWorkspace,gh_pop_get_data) |
|
| 137 |
+importFrom(flowWorkspace,gh_pop_get_stats) |
|
| 138 |
+importFrom(flowWorkspace,gh_pop_is_hidden) |
|
| 139 |
+importFrom(flowWorkspace,gh_pop_is_negated) |
|
| 141 | 140 |
importFrom(flowWorkspace,gs_clone) |
| 142 | 141 |
importFrom(flowWorkspace,gs_get_compensation_internal) |
| 143 |
-importFrom(flowWorkspace,gs_get_parent) |
|
| 144 |
-importFrom(flowWorkspace,gs_set_node_name) |
|
| 142 |
+importFrom(flowWorkspace,gs_pop_get_parent) |
|
| 143 |
+importFrom(flowWorkspace,gs_pop_set_name) |
|
| 144 |
+importFrom(flowWorkspace,gs_split_by_tree) |
|
| 145 |
+importFrom(flowWorkspace,gs_update_channels) |
|
| 145 | 146 |
importFrom(flowWorkspace,keyword) |
| 146 | 147 |
importFrom(flowWorkspace,load_gs) |
| 147 | 148 |
importFrom(flowWorkspace,logicleGml2_trans) |
| ... | ... |
@@ -157,7 +158,6 @@ importFrom(flowWorkspace,show) |
| 157 | 158 |
importFrom(flowWorkspace,swap_data_cols) |
| 158 | 159 |
importFrom(flowWorkspace,transform) |
| 159 | 160 |
importFrom(flowWorkspace,transformerList) |
| 160 |
-importFrom(flowWorkspace,updateChannels) |
|
| 161 | 161 |
importFrom(ggcyto,rescale_gate) |
| 162 | 162 |
importFrom(grDevices,rgb) |
| 163 | 163 |
importFrom(graph,"nodeData<-") |
mikejiang authored on 15/04/2019 18:13:32
| ... | ... |
@@ -1,54 +1,48 @@ |
| 1 | 1 |
# Generated by roxygen2: do not edit by hand |
| 2 | 2 |
|
| 3 |
-S3method(cytobank2GatingSet,cytobankExperiment) |
|
| 4 |
-S3method(cytobank2GatingSet,default) |
|
| 3 |
+S3method(cytobank_to_gatingset,cytobank_experiment) |
|
| 4 |
+S3method(cytobank_to_gatingset,default) |
|
| 5 | 5 |
S3method(extend,ellipsoidGate) |
| 6 | 6 |
S3method(extend,polygonGate) |
| 7 | 7 |
S3method(extend,rectangleGate) |
| 8 |
-S3method(getCompensationMatrices,cytobankExperiment) |
|
| 9 |
-S3method(getCompensationMatrices,graphGML) |
|
| 10 |
-S3method(getTransformations,cytobankExperiment) |
|
| 11 |
-S3method(getTransformations,graphGML) |
|
| 12 |
-S3method(openWorkspace,character) |
|
| 13 |
-S3method(print,cytobankExperiment) |
|
| 8 |
+S3method(print,cytobank_experiment) |
|
| 14 | 9 |
export(CytoML.par.get) |
| 15 | 10 |
export(CytoML.par.set) |
| 16 | 11 |
export(GatingSet2cytobank) |
| 17 | 12 |
export(GatingSet2flowJo) |
| 13 |
+export(ce_get_cmpensations) |
|
| 14 |
+export(ce_get_transformations) |
|
| 18 | 15 |
export(closeWorkspace) |
| 19 |
-export(compare.counts) |
|
| 20 | 16 |
export(cytobank2GatingSet) |
| 21 | 17 |
export(cytobankExperiment) |
| 18 |
+export(cytobank_to_gatingset) |
|
| 19 |
+export(diva_get_sample_groups) |
|
| 20 |
+export(diva_get_samples) |
|
| 22 | 21 |
export(extend) |
| 23 |
-export(getCompensationMatrices) |
|
| 22 |
+export(fj_ws_get_keywords) |
|
| 23 |
+export(fj_ws_get_sample_groups) |
|
| 24 |
+export(fj_ws_get_samples) |
|
| 25 |
+export(flowjo_to_gatingset) |
|
| 26 |
+export(flowjo_ws_close) |
|
| 27 |
+export(gatingset_to_cytobank) |
|
| 28 |
+export(gatingset_to_flowjo) |
|
| 24 | 29 |
export(getFJWSubsetIndices) |
| 25 | 30 |
export(getKeywords) |
| 26 | 31 |
export(getSampleGroups) |
| 27 | 32 |
export(getSamples) |
| 28 |
-export(getTransformations) |
|
| 33 |
+export(gs_compare_cytobank_counts) |
|
| 29 | 34 |
export(openDiva) |
| 30 |
-export(openWorkspace) |
|
| 35 |
+export(open_cytobank_experiment) |
|
| 36 |
+export(open_diva_xml) |
|
| 37 |
+export(open_flowjo_xml) |
|
| 31 | 38 |
export(parseWorkspace) |
| 32 |
-export(read.gatingML.cytobank) |
|
| 33 |
-exportClasses(divaWorkspace) |
|
| 34 |
-exportClasses(flowJoWorkspace) |
|
| 35 |
-exportClasses(graphGML) |
|
| 39 |
+exportClasses(diva_workspace) |
|
| 40 |
+exportClasses(flowjo_workspace) |
|
| 36 | 41 |
exportMethods(GatingSet) |
| 37 |
-exportMethods(closeWorkspace) |
|
| 38 | 42 |
exportMethods(colnames) |
| 39 |
-exportMethods(compensate) |
|
| 40 |
-exportMethods(gating) |
|
| 41 |
-exportMethods(getChildren) |
|
| 42 |
-exportMethods(getGate) |
|
| 43 |
-exportMethods(getKeywords) |
|
| 44 |
-exportMethods(getNodes) |
|
| 45 |
-exportMethods(getParent) |
|
| 46 |
-exportMethods(getSampleGroups) |
|
| 47 |
-exportMethods(getSamples) |
|
| 48 | 43 |
exportMethods(markernames) |
| 49 | 44 |
exportMethods(pData) |
| 50 | 45 |
exportMethods(parseWorkspace) |
| 51 |
-exportMethods(plot) |
|
| 52 | 46 |
exportMethods(sampleNames) |
| 53 | 47 |
exportMethods(show) |
| 54 | 48 |
import(data.table) |
| ... | ... |
@@ -154,7 +148,6 @@ importFrom(flowWorkspace,logicleGml2_trans) |
| 154 | 148 |
importFrom(flowWorkspace,logicle_trans) |
| 155 | 149 |
importFrom(flowWorkspace,logtGml2_trans) |
| 156 | 150 |
importFrom(flowWorkspace,markernames) |
| 157 |
-importFrom(flowWorkspace,openWorkspace) |
|
| 158 | 151 |
importFrom(flowWorkspace,pData) |
| 159 | 152 |
importFrom(flowWorkspace,recompute) |
| 160 | 153 |
importFrom(flowWorkspace,sampleNames) |
mikejiang authored on 08/04/2019 18:52:45
| ... | ... |
@@ -125,7 +125,6 @@ importFrom(flowWorkspace,GatingSetList) |
| 125 | 125 |
importFrom(flowWorkspace,add) |
| 126 | 126 |
importFrom(flowWorkspace,asinh_Gml2) |
| 127 | 127 |
importFrom(flowWorkspace,asinhtGml2_trans) |
| 128 |
-importFrom(flowWorkspace,clone) |
|
| 129 | 128 |
importFrom(flowWorkspace,compute_timestep) |
| 130 | 129 |
importFrom(flowWorkspace,extract_cluster_pop_name_from_node) |
| 131 | 130 |
importFrom(flowWorkspace,filterObject) |
| ... | ... |
@@ -133,19 +132,22 @@ importFrom(flowWorkspace,fix_channel_slash) |
| 133 | 132 |
importFrom(flowWorkspace,flow_trans) |
| 134 | 133 |
importFrom(flowWorkspace,getChildren) |
| 135 | 134 |
importFrom(flowWorkspace,getCompensationMatrices) |
| 136 |
-importFrom(flowWorkspace,getData) |
|
| 137 | 135 |
importFrom(flowWorkspace,getGate) |
| 138 | 136 |
importFrom(flowWorkspace,getNodes) |
| 139 | 137 |
importFrom(flowWorkspace,getParent) |
| 140 |
-importFrom(flowWorkspace,getPopStats) |
|
| 141 |
-importFrom(flowWorkspace,getTotal) |
|
| 142 | 138 |
importFrom(flowWorkspace,getTransformations) |
| 143 | 139 |
importFrom(flowWorkspace,gh_check_cluster_node) |
| 144 | 140 |
importFrom(flowWorkspace,gh_get_cluster_labels) |
| 141 |
+importFrom(flowWorkspace,gh_get_count) |
|
| 142 |
+importFrom(flowWorkspace,gh_get_data) |
|
| 143 |
+importFrom(flowWorkspace,gh_get_pop_stats) |
|
| 144 |
+importFrom(flowWorkspace,gh_is_hidden) |
|
| 145 |
+importFrom(flowWorkspace,gh_is_negated) |
|
| 145 | 146 |
importFrom(flowWorkspace,groupByTree) |
| 147 |
+importFrom(flowWorkspace,gs_clone) |
|
| 146 | 148 |
importFrom(flowWorkspace,gs_get_compensation_internal) |
| 147 |
-importFrom(flowWorkspace,isHidden) |
|
| 148 |
-importFrom(flowWorkspace,isNegated) |
|
| 149 |
+importFrom(flowWorkspace,gs_get_parent) |
|
| 150 |
+importFrom(flowWorkspace,gs_set_node_name) |
|
| 149 | 151 |
importFrom(flowWorkspace,keyword) |
| 150 | 152 |
importFrom(flowWorkspace,load_gs) |
| 151 | 153 |
importFrom(flowWorkspace,logicleGml2_trans) |
mikejiang authored on 05/04/2019 18:09:08
mikejiang authored on 02/04/2019 04:58:33
| ... | ... |
@@ -11,6 +11,8 @@ S3method(getTransformations,cytobankExperiment) |
| 11 | 11 |
S3method(getTransformations,graphGML) |
| 12 | 12 |
S3method(openWorkspace,character) |
| 13 | 13 |
S3method(print,cytobankExperiment) |
| 14 |
+export(CytoML.par.get) |
|
| 15 |
+export(CytoML.par.set) |
|
| 14 | 16 |
export(GatingSet2cytobank) |
| 15 | 17 |
export(GatingSet2flowJo) |
| 16 | 18 |
export(closeWorkspace) |
mikejiang authored on 29/03/2019 19:07:38
| ... | ... |
@@ -131,7 +131,6 @@ importFrom(flowWorkspace,fix_channel_slash) |
| 131 | 131 |
importFrom(flowWorkspace,flow_trans) |
| 132 | 132 |
importFrom(flowWorkspace,getChildren) |
| 133 | 133 |
importFrom(flowWorkspace,getCompensationMatrices) |
| 134 |
-importFrom(flowWorkspace,getCompensationObj) |
|
| 135 | 134 |
importFrom(flowWorkspace,getData) |
| 136 | 135 |
importFrom(flowWorkspace,getGate) |
| 137 | 136 |
importFrom(flowWorkspace,getNodes) |
| ... | ... |
@@ -142,6 +141,7 @@ importFrom(flowWorkspace,getTransformations) |
| 142 | 141 |
importFrom(flowWorkspace,gh_check_cluster_node) |
| 143 | 142 |
importFrom(flowWorkspace,gh_get_cluster_labels) |
| 144 | 143 |
importFrom(flowWorkspace,groupByTree) |
| 144 |
+importFrom(flowWorkspace,gs_get_compensation_internal) |
|
| 145 | 145 |
importFrom(flowWorkspace,isHidden) |
| 146 | 146 |
importFrom(flowWorkspace,isNegated) |
| 147 | 147 |
importFrom(flowWorkspace,keyword) |
mikejiang authored on 22/03/2019 21:02:35
mikejiang authored on 21/03/2019 19:07:47
| ... | ... |
@@ -1,5 +1,54 @@ |
| 1 | 1 |
# Generated by roxygen2: do not edit by hand |
| 2 | 2 |
|
| 3 |
+S3method(cytobank2GatingSet,cytobankExperiment) |
|
| 4 |
+S3method(cytobank2GatingSet,default) |
|
| 5 |
+S3method(extend,ellipsoidGate) |
|
| 6 |
+S3method(extend,polygonGate) |
|
| 7 |
+S3method(extend,rectangleGate) |
|
| 8 |
+S3method(getCompensationMatrices,cytobankExperiment) |
|
| 9 |
+S3method(getCompensationMatrices,graphGML) |
|
| 10 |
+S3method(getTransformations,cytobankExperiment) |
|
| 11 |
+S3method(getTransformations,graphGML) |
|
| 12 |
+S3method(openWorkspace,character) |
|
| 13 |
+S3method(print,cytobankExperiment) |
|
| 14 |
+export(GatingSet2cytobank) |
|
| 15 |
+export(GatingSet2flowJo) |
|
| 16 |
+export(closeWorkspace) |
|
| 17 |
+export(compare.counts) |
|
| 18 |
+export(cytobank2GatingSet) |
|
| 19 |
+export(cytobankExperiment) |
|
| 20 |
+export(extend) |
|
| 21 |
+export(getCompensationMatrices) |
|
| 22 |
+export(getFJWSubsetIndices) |
|
| 23 |
+export(getKeywords) |
|
| 24 |
+export(getSampleGroups) |
|
| 25 |
+export(getSamples) |
|
| 26 |
+export(getTransformations) |
|
| 27 |
+export(openDiva) |
|
| 28 |
+export(openWorkspace) |
|
| 29 |
+export(parseWorkspace) |
|
| 30 |
+export(read.gatingML.cytobank) |
|
| 31 |
+exportClasses(divaWorkspace) |
|
| 32 |
+exportClasses(flowJoWorkspace) |
|
| 33 |
+exportClasses(graphGML) |
|
| 34 |
+exportMethods(GatingSet) |
|
| 35 |
+exportMethods(closeWorkspace) |
|
| 36 |
+exportMethods(colnames) |
|
| 37 |
+exportMethods(compensate) |
|
| 38 |
+exportMethods(gating) |
|
| 39 |
+exportMethods(getChildren) |
|
| 40 |
+exportMethods(getGate) |
|
| 41 |
+exportMethods(getKeywords) |
|
| 42 |
+exportMethods(getNodes) |
|
| 43 |
+exportMethods(getParent) |
|
| 44 |
+exportMethods(getSampleGroups) |
|
| 45 |
+exportMethods(getSamples) |
|
| 46 |
+exportMethods(markernames) |
|
| 47 |
+exportMethods(pData) |
|
| 48 |
+exportMethods(parseWorkspace) |
|
| 49 |
+exportMethods(plot) |
|
| 50 |
+exportMethods(sampleNames) |
|
| 51 |
+exportMethods(show) |
|
| 3 | 52 |
import(data.table) |
| 4 | 53 |
importClassesFrom(Biobase,AssayData) |
| 5 | 54 |
importClassesFrom(XML,XMLInternalDocument) |
mikejiang authored on 20/03/2019 22:39:17
| ... | ... |
@@ -1,54 +1,5 @@ |
| 1 | 1 |
# Generated by roxygen2: do not edit by hand |
| 2 | 2 |
|
| 3 |
-S3method(cytobank2GatingSet,cytobankExperiment) |
|
| 4 |
-S3method(cytobank2GatingSet,default) |
|
| 5 |
-S3method(extend,ellipsoidGate) |
|
| 6 |
-S3method(extend,polygonGate) |
|
| 7 |
-S3method(extend,rectangleGate) |
|
| 8 |
-S3method(getCompensationMatrices,cytobankExperiment) |
|
| 9 |
-S3method(getCompensationMatrices,graphGML) |
|
| 10 |
-S3method(getTransformations,cytobankExperiment) |
|
| 11 |
-S3method(getTransformations,graphGML) |
|
| 12 |
-S3method(openWorkspace,character) |
|
| 13 |
-S3method(print,cytobankExperiment) |
|
| 14 |
-export(GatingSet2cytobank) |
|
| 15 |
-export(GatingSet2flowJo) |
|
| 16 |
-export(closeWorkspace) |
|
| 17 |
-export(compare.counts) |
|
| 18 |
-export(cytobank2GatingSet) |
|
| 19 |
-export(cytobankExperiment) |
|
| 20 |
-export(extend) |
|
| 21 |
-export(getCompensationMatrices) |
|
| 22 |
-export(getFJWSubsetIndices) |
|
| 23 |
-export(getKeywords) |
|
| 24 |
-export(getSampleGroups) |
|
| 25 |
-export(getSamples) |
|
| 26 |
-export(getTransformations) |
|
| 27 |
-export(openDiva) |
|
| 28 |
-export(openWorkspace) |
|
| 29 |
-export(parseWorkspace) |
|
| 30 |
-export(read.gatingML.cytobank) |
|
| 31 |
-exportClasses(divaWorkspace) |
|
| 32 |
-exportClasses(flowJoWorkspace) |
|
| 33 |
-exportClasses(graphGML) |
|
| 34 |
-exportMethods(GatingSet) |
|
| 35 |
-exportMethods(closeWorkspace) |
|
| 36 |
-exportMethods(colnames) |
|
| 37 |
-exportMethods(compensate) |
|
| 38 |
-exportMethods(gating) |
|
| 39 |
-exportMethods(getChildren) |
|
| 40 |
-exportMethods(getGate) |
|
| 41 |
-exportMethods(getKeywords) |
|
| 42 |
-exportMethods(getNodes) |
|
| 43 |
-exportMethods(getParent) |
|
| 44 |
-exportMethods(getSampleGroups) |
|
| 45 |
-exportMethods(getSamples) |
|
| 46 |
-exportMethods(markernames) |
|
| 47 |
-exportMethods(pData) |
|
| 48 |
-exportMethods(parseWorkspace) |
|
| 49 |
-exportMethods(plot) |
|
| 50 |
-exportMethods(sampleNames) |
|
| 51 |
-exportMethods(show) |
|
| 52 | 3 |
import(data.table) |
| 53 | 4 |
importClassesFrom(Biobase,AssayData) |
| 54 | 5 |
importClassesFrom(XML,XMLInternalDocument) |
mikejiang authored on 20/03/2019 20:06:07
| ... | ... |
@@ -9,24 +9,36 @@ S3method(getCompensationMatrices,cytobankExperiment) |
| 9 | 9 |
S3method(getCompensationMatrices,graphGML) |
| 10 | 10 |
S3method(getTransformations,cytobankExperiment) |
| 11 | 11 |
S3method(getTransformations,graphGML) |
| 12 |
+S3method(openWorkspace,character) |
|
| 12 | 13 |
S3method(print,cytobankExperiment) |
| 13 | 14 |
export(GatingSet2cytobank) |
| 14 | 15 |
export(GatingSet2flowJo) |
| 16 |
+export(closeWorkspace) |
|
| 15 | 17 |
export(compare.counts) |
| 16 | 18 |
export(cytobank2GatingSet) |
| 17 | 19 |
export(cytobankExperiment) |
| 18 | 20 |
export(extend) |
| 19 | 21 |
export(getCompensationMatrices) |
| 22 |
+export(getFJWSubsetIndices) |
|
| 23 |
+export(getKeywords) |
|
| 24 |
+export(getSampleGroups) |
|
| 25 |
+export(getSamples) |
|
| 20 | 26 |
export(getTransformations) |
| 21 | 27 |
export(openDiva) |
| 28 |
+export(openWorkspace) |
|
| 29 |
+export(parseWorkspace) |
|
| 22 | 30 |
export(read.gatingML.cytobank) |
| 23 | 31 |
exportClasses(divaWorkspace) |
| 32 |
+exportClasses(flowJoWorkspace) |
|
| 24 | 33 |
exportClasses(graphGML) |
| 34 |
+exportMethods(GatingSet) |
|
| 35 |
+exportMethods(closeWorkspace) |
|
| 25 | 36 |
exportMethods(colnames) |
| 26 | 37 |
exportMethods(compensate) |
| 27 | 38 |
exportMethods(gating) |
| 28 | 39 |
exportMethods(getChildren) |
| 29 | 40 |
exportMethods(getGate) |
| 41 |
+exportMethods(getKeywords) |
|
| 30 | 42 |
exportMethods(getNodes) |
| 31 | 43 |
exportMethods(getParent) |
| 32 | 44 |
exportMethods(getSampleGroups) |
| ... | ... |
@@ -39,7 +51,7 @@ exportMethods(sampleNames) |
| 39 | 51 |
exportMethods(show) |
| 40 | 52 |
import(data.table) |
| 41 | 53 |
importClassesFrom(Biobase,AssayData) |
| 42 |
-importClassesFrom(flowWorkspace,flowJoWorkspace) |
|
| 54 |
+importClassesFrom(XML,XMLInternalDocument) |
|
| 43 | 55 |
importClassesFrom(graph,graph) |
| 44 | 56 |
importClassesFrom(graph,graphBase) |
| 45 | 57 |
importClassesFrom(graph,graphNEL) |
| ... | ... |
@@ -58,6 +70,7 @@ importFrom(Rgraphviz,layoutGraph) |
| 58 | 70 |
importFrom(Rgraphviz,renderGraph) |
| 59 | 71 |
importFrom(XML,"xmlAttrs<-") |
| 60 | 72 |
importFrom(XML,addChildren) |
| 73 |
+importFrom(XML,free) |
|
| 61 | 74 |
importFrom(XML,getNodeSet) |
| 62 | 75 |
importFrom(XML,newXMLNode) |
| 63 | 76 |
importFrom(XML,saveXML) |
| ... | ... |
@@ -77,6 +90,9 @@ importFrom(XML,xpathApply) |
| 77 | 90 |
importFrom(XML,xpathSApply) |
| 78 | 91 |
importFrom(base64enc,base64decode) |
| 79 | 92 |
importFrom(base64enc,base64encode) |
| 93 |
+importFrom(dplyr,"%>%") |
|
| 94 |
+importFrom(dplyr,do) |
|
| 95 |
+importFrom(dplyr,group_by) |
|
| 80 | 96 |
importFrom(flowCore,"colnames<-") |
| 81 | 97 |
importFrom(flowCore,"identifier<-") |
| 82 | 98 |
importFrom(flowCore,"parameters<-") |
| ... | ... |
@@ -121,8 +137,6 @@ importFrom(flowWorkspace,getGate) |
| 121 | 137 |
importFrom(flowWorkspace,getNodes) |
| 122 | 138 |
importFrom(flowWorkspace,getParent) |
| 123 | 139 |
importFrom(flowWorkspace,getPopStats) |
| 124 |
-importFrom(flowWorkspace,getSampleGroups) |
|
| 125 |
-importFrom(flowWorkspace,getSamples) |
|
| 126 | 140 |
importFrom(flowWorkspace,getTotal) |
| 127 | 141 |
importFrom(flowWorkspace,getTransformations) |
| 128 | 142 |
importFrom(flowWorkspace,gh_check_cluster_node) |
| ... | ... |
@@ -136,8 +150,8 @@ importFrom(flowWorkspace,logicleGml2_trans) |
| 136 | 150 |
importFrom(flowWorkspace,logicle_trans) |
| 137 | 151 |
importFrom(flowWorkspace,logtGml2_trans) |
| 138 | 152 |
importFrom(flowWorkspace,markernames) |
| 153 |
+importFrom(flowWorkspace,openWorkspace) |
|
| 139 | 154 |
importFrom(flowWorkspace,pData) |
| 140 |
-importFrom(flowWorkspace,parseWorkspace) |
|
| 141 | 155 |
importFrom(flowWorkspace,recompute) |
| 142 | 156 |