Generate HTML files and all image files (plots) from the result
of ipcaps. The clustering result is shown as a tree rendering
by the online Google Organizational Chart library. Note that the Internet is
required to view the HTML files.
save.plots(output.dir)
| output.dir | A result directory as the |
|---|
NULL
After running, this function generates all plots and saves as image files in the
sub-directory 'images'. It calls save.plots.cluster.html,
save.eigenplots.html, and save.plots.label.html
to generate all HTML files.
# Importantly, bed file, bim file, and fam file are required # Use the example files embedded in the package BED.file <- system.file("extdata","ipcaps_example.bed",package="IPCAPS") LABEL.file <- system.file("extdata","ipcaps_example_individuals.txt.gz",package="IPCAPS") my.cluster <- ipcaps(bed=BED.file,label.file=LABEL.file,lab.col=2,out=tempdir())#> Running ... IPCAPS #> output: /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk #> label file: /private/var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T/RtmpYTlCbr/temp_libpath1351142c69ef5/IPCAPS/extdata/ipcaps_example_individuals.txt.gz #> label column: 2 #> threshold: 0.18 #> minimum Fst: 8e-04 #> maximum thread: 1 #> method: mix #> bed: /private/var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T/RtmpYTlCbr/temp_libpath1351142c69ef5/IPCAPS/extdata/ipcaps_example.bed #> minimum in group: 20 #> data type: snp #> missing: NA #> In preprocessing step #> Note: the directory '/var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk' is existed. #> The result files will be saved to this directory: /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5 #> Input data: 103 individuals, 2000 markers #> Start calculating #> Node 1: Start the process #> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/condition.RData #> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/rawdata.RData #> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node1.RData #> Node 1: Check for splitting #> Node 1: Reducing matrix #> Node 1: EigenFit = 0.652486925995028, Threshold = 0.18, no. significant PCs = 3 #> Node 1: Start clustering #> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node1.RData #> Node 1: done for clustering #> Time difference of 0.09902692 secs #> Node 1: Checking Fst of group 1 and group 2 #> Node 1: Checking Fst of group 1 and group 3 #> Node 1: Checking Fst of group 1 and group 4 #> Node 1: Checking Fst of group 2 and group 3 #> Node 1: Checking Fst of group 2 and group 4 #> Node 1: Checking Fst of group 3 and group 4 #> Node 1 times took 0.301676034927368 secs #> Node 1: 103 individuals were splitted into: 4 groups #> Node 1: Return status 0 #> Node 1: Split to sub-nodes #> Node 1: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node2.RData #> Node 1: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node3.RData #> Node 1: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node4.RData #> Node 1: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node5.RData #> Node 1: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 1: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 1: Done! #> Time difference of 0.4612188 secs #> Node 2: Start the process #> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/condition.RData #> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/rawdata.RData #> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node2.RData #> Node 2: Check for splitting #> Node 2: A number of node is lower than the minimum number (20), therefore split was not performed #> Node 2: Return status 1 #> Node 2: No split was performed, Status=1 #> Node 2: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/leafnode.RData #> Node 2: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 2: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 2: Done! #> Time difference of 0.03531194 secs #> Node 3: Start the process #> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/condition.RData #> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/rawdata.RData #> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node3.RData #> Node 3: Check for splitting #> Node 3: A number of node is lower than the minimum number (20), therefore split was not performed #> Node 3: Return status 1 #> Node 3: No split was performed, Status=1 #> Node 3: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/leafnode.RData #> Node 3: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 3: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 3: Done! #> Time difference of 0.036479 secs #> Node 4: Start the process #> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/condition.RData #> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/rawdata.RData #> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node4.RData #> Node 4: Check for splitting #> Node 4: A number of node is lower than the minimum number (20), therefore split was not performed #> Node 4: Return status 1 #> Node 4: No split was performed, Status=1 #> Node 4: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/leafnode.RData #> Node 4: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 4: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 4: Done! #> Time difference of 0.03094506 secs #> Node 5: Start the process #> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/condition.RData #> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/rawdata.RData #> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node5.RData #> Node 5: Check for splitting #> Node 5: Reducing matrix #> Node 5: EigenFit = 0.343228072167861, Threshold = 0.18, no. significant PCs = 3 #> Node 5: Start clustering #> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node5.RData #> Node 5: done for clustering #> Time difference of 0.1046531 secs #> Node 5: Checking Fst of group 1 and group 2 #> Node 5 times took 0.154040098190308 secs #> Node 5: 100 individuals were splitted into: 2 groups #> Node 5: Return status 0 #> Node 5: Split to sub-nodes #> Node 5: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node6.RData #> Node 5: Saving /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node7.RData #> Node 5: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 5: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 5: Done! #> Time difference of 0.3086112 secs #> Node 6: Start the process #> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/condition.RData #> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/rawdata.RData #> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node6.RData #> Node 6: Check for splitting #> Node 6: Reducing matrix #> Node 6: EigenFit = 0.0221170820186458, Threshold = 0.18, no. significant PCs = #> Node 6: No split was performed because EigenFit is lower than threshold #> Node 6: Return status 1 #> Node 6: No split was performed, Status=1 #> Node 6: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/leafnode.RData #> Node 6: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 6: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 6: Done! #> Time difference of 0.1142409 secs #> Node 7: Start the process #> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/condition.RData #> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/rawdata.RData #> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/node7.RData #> Node 7: Check for splitting #> Node 7: Reducing matrix #> Node 7: EigenFit = 0.0367738545252401, Threshold = 0.18, no. significant PCs = #> Node 7: No split was performed because EigenFit is lower than threshold #> Node 7: Return status 1 #> Node 7: No split was performed, Status=1 #> Node 7: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/leafnode.RData #> Node 7: Loading /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 7: Updating /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/RData/tree.RData #> Node 7: Done! #> Time difference of 0.1115348 secs #> In post process step #> Exporting node 2 as group 1 #> Exporting node 3 as group 2 #> Exporting node 4 as group 3 #> Exporting node 6 as group 4 #> Exporting node 7 as group 5 #> Note: save as /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5/groups.txt#> The result files were saved at: /var/folders/sp/hhmj9xvx53z4g4dktf5f503r0000gp/T//Rtmpvv9uwk/cluster_output5 #> Total runtime is 2.23816299438477 sec