Sploidyplot (#169)

* resolved speckliness with a new alt plot, its not yet the default, but it works, can be run with --alt_plot flag * fixing #153 - suprise suprise, smudgeplot package already has a function for weighted quantiles :-) * keeping track of all the testing and proof of concept functions, most notably, local agregation for the alt plot * quantile filtering is now applied after coverage filter * adding the first draft of peak fitting using centrality * adding code for popart plot * added peak agregation algorithm in the main smudgeplot source code * adding python funciton that generates the smudge container given coverges * the new version is nearly working the only missing bit is the smudgeplot itself * the over-very-lnog time playiung around stuff * histogramless, but working version of smudgeplot ORIEL * updating readme with the new imlpemenation * giant cleanup - removing the R package and simplifying the installation * fixing / simplifying installation instructions * streamlining interface and allowing for plotting parameters to be passed to all subprocess * making title work * fixing interface problem to call hetmer module; adding kmer numbers to the log; adding exploration of 1/2 of the final coverage, but it still does not solve the problem of autotetraploids * adding parametrised coverage range to explore * adding error filtering step that stops inference of coverage for datasets with very high proportion of errors (>0.8) * adding small explorations on alternative centralities * making fix * small fixes
KamilSJaron · Nov 4, 2024 · 6c1e48d · 6c1e48d
1 parent f12ec1e
commit 6c1e48d
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diff --git a/.gitignore b/.gitignore
@@ -3,5 +3,7 @@ figures
 playground
 docs
 exec/PloidyPlot
+exec/hetmers
 *.o
 .DS_Store
+smu2text_smu
diff --git a/DESCRIPTION b/DESCRIPTION
diff --git a/Makefile b/Makefile
@@ -1,30 +1,23 @@
 # PATH for libraries is guessed
-RPACKAGE = smudgeplot
-$(eval RPATH := $(shell Rscript -e "noquote(.libPaths())" | tail -1 | cut -f 2 -d ' '))
 CFLAGS = -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing
 
 ifndef INSTALL_PREFIX
     INSTALL_PREFIX = /usr/local
 endif
 
-R_INSTALLATION = $(RPATH)/$(RPACKAGE)
-HET_KMERS_INST = $(INSTALL_PREFIX)/bin/smudgeplot.py $(INSTALL_PREFIX)/bin/PloidyPlot
-SMUDGEPLOT_INST = $(INSTALL_PREFIX)/bin/smudgeplot_plot.R
+HET_KMERS_INST = $(INSTALL_PREFIX)/bin/smudgeplot.py $(INSTALL_PREFIX)/bin/hetmers
+SMUDGEPLOT_INST = $(INSTALL_PREFIX)/bin/smudgeplot_plot.R $(INSTALL_PREFIX)/bin/centrality_plot.R
 
 .PHONY : install
-install : $(HET_KMERS_INST) $(SMUDGEPLOT_INST) $(CUTOFF_INST) $(R_INSTALLATION) 
-# - removing the R package from the list
+install : $(HET_KMERS_INST) $(SMUDGEPLOT_INST) $(CUTOFF_INST) 
 
 $(INSTALL_PREFIX)/bin/% : exec/%
 	install -C $< $(INSTALL_PREFIX)/bin
 
-$(R_INSTALLATION) : R/*
-	Rscript install.R
-
-exec/PloidyPlot: src_ploidyplot/PloidyPlot.c src_ploidyplot/libfastk.c src_ploidyplot/libfastk.h src_ploidyplot/matrix.c src_ploidyplot/matrix.h
+exec/hetmers: src_ploidyplot/PloidyPlot.c src_ploidyplot/libfastk.c src_ploidyplot/libfastk.h src_ploidyplot/matrix.c src_ploidyplot/matrix.h
 	gcc $(CFLAGS) -o $@ src_ploidyplot/PloidyPlot.c src_ploidyplot/libfastk.c src_ploidyplot/matrix.c -lpthread -lm
 
 
 .PHONY : clean
 clean :
-	rm -f exec/PloidyPlot
+	rm -f exec/hetmers
diff --git a/NAMESPACE b/NAMESPACE
diff --git a/R/annotate_peaks.R b/R/annotate_peaks.R
diff --git a/R/annotate_summits.R b/R/annotate_summits.R
diff --git a/R/bw.nrdW.R b/R/bw.nrdW.R
diff --git a/R/coverage_histogram.R b/R/coverage_histogram.R
diff --git a/R/estimate_1n_coverage_1d_subsets.R b/R/estimate_1n_coverage_1d_subsets.R
diff --git a/R/estimate_1n_coverage_highest_peak.R b/R/estimate_1n_coverage_highest_peak.R
diff --git a/R/filter_peak_sizes.R b/R/filter_peak_sizes.R
diff --git a/R/filter_peaks.R b/R/filter_peaks.R
diff --git a/R/generate_summary.R b/R/generate_summary.R
diff --git a/R/get_1d_peaks.R b/R/get_1d_peaks.R