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Copy pathdiffloopFitHiChIPToLonginteract_threshold.py
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diffloopFitHiChIPToLonginteract_threshold.py
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#!/Users/jra/miniconda3/bin/python3
import sys
import pandas as pd
import numpy as np
import subprocess
pd.set_option('mode.chained_assignment', None)
userInputFile = sys.argv[1]
inputFile = pd.read_csv(userInputFile, sep='\t')
'''
Header from fithichip diffloops output
chr1 start1 end1 chr2 start2 end2 C1_R1_RawCC C1_R1_QVal C1_R2_RawCC C1_R2_QVal
C2_R1_RawCC C2_R1_QVal C2_R2_RawCC C2_R2_QVal logFC logCPM PValue FDR C1_SigRepl C2_SigRepl
'''
df = inputFile[['chr1','start1','end1','chr2','start2','end2','logFC','FDR']]
df["score"] = 10 # don't need this anymore
#df.drop(df[df['score']<5].index, inplace=True) #remove rows with less than 5 total read alignments
cutoff = 0.05 # min FDR cutoff
df["color"] = np.where( df['logFC'] < 0, "246,133,50", "38,103,153" ) # condition, true, false
#df["color"] = np.where( df['logFC'] < 0, "1,160,115", "158,53,158" ) # for WT ESC vs EpiLC
df["color"] = np.where( df['FDR'] < cutoff, df["color"], "222,222,222" ) # set non-sigificant loops to grey
df["NA"] = "." # fill in unnecessary columns
df["colour_calc"] = df["score"] # was previously used for gradient colours
df = df.rename(columns={'chr1': '#chr', 'start1': 'start', 'end1': 'end', 'start1': 'start'})
df_to_print = df[['#chr', 'start', 'end2', 'NA', 'score', 'colour_calc', 'NA', 'color', '#chr', 'start', 'end', 'NA', 'NA', 'chr2', 'start2', 'end2', 'NA', 'NA']]
#print(df.head(5))
#print(df_to_print.head(2))
outTable = "%s_diffloops_x5_FDR_colors_thresh.bed" % (userInputFile)
df_to_print.to_csv(outTable, sep='\t', header=False, index=False)
'''
> library(diffloopdata)
> library(ggplot2)
> library(GenomicRanges)
> library(ggrepel)
> library(DESeq2)
> beddir <- "/scratch/hicpro_all_samples_full_depth/test6"
> samples <- c("D4_DnmtWT_rep1.filt.intra","D4_DnmtWT_rep2.filt.intra","D4_DnmtTKO_rep1.filt.intra","D4_DnmtTKO_rep2.filt.intra")
> FullR1 <- loopsMake(beddir,samples=samples)
dim(FullR1)
anchors interactions samples colData rowData
1 52310 636656 4 2 1
> FullR1_mango <- mangoCorrection(FullR1, FDR = 0.05)
dim(FullR1_mango)
^C
>
>
>
> FullR1_mango <- mangoCorrection(FullR1, FDR = 0.05)
>
> dim(FullR1_mango)
anchors interactions samples colData rowData
1 50232 340992 4 2 3
> p1 <- loopDistancePlot(FullR1_mango)
> p1
>
>
>
> view(p1)
Error in view(p1) : could not find function "view"
> p1.show()
Error in p1.show() : could not find function "p1.show"
> show(p1)
>
>
> pdf("test_plot.pdf")
> plot(p1)
> dev.off()
pdf
2
>
>
> loopMetrics(FullR1_mango)
D4_DnmtWT_rep1.filt.intra D4_DnmtWT_rep2.filt.intra
unique 268650 276181
D4_DnmtTKO_rep1.filt.intra D4_DnmtTKO_rep2.filt.intra
unique 251928 257501
> pcp1dat <- FullR1_mango
> pcp1dat@colData$sizeFactor <- 1
> pcp1 <- pcaPlot(pcp1dat) + geom_text_repel(aes(label=samples)) +
scale_x_continuous(limits = c(-140, 230)) + ggtitle("PC Plot with no Size Factor Correction") +
theme(legend.position="none")
>
> pdf("test_plot2.pdf")
> plot(pcp1)
Warning messages:
1: Removed 1 rows containing missing values (geom_point).
2: Removed 1 rows containing missing values (geom_text_repel).
> dev.off()
pdf
2
> samples
[1] "D4_DnmtWT_rep1.filt.intra" "D4_DnmtWT_rep2.filt.intra"
[3] "D4_DnmtTKO_rep1.filt.intra" "D4_DnmtTKO_rep2.filt.intra"
> pcp1 <- pcaPlot(pcp1dat) + geom_text_repel(aes(label=samples)) +
scale_x_continuous(ggtitle("PC Plot with no Size Factor Correction") +
theme(legend.position="none")
+
+
+
+
> pcp1 <- pcaPlot(pcp1dat) + geom_text_repel(aes(label=samples)) +
+
theme(legend.position="none")
Error in `+.gg`:
! Cannot use `+.gg()` with a single argument. Did you accidentally put + on a new line?
Run `rlang::last_error()` to see where the error occurred.
>
> pcp1 <- pcaPlot(pcp1dat) + geom_text_repel(aes(label=samples)) +
theme(legend.position="none")
> pdf("test_plot2.pdf")
> plot(pcp1)
> dev.off()
pdf
2
> pcp2 <-pcaPlot(qc_filt) + geom_text_repel(aes(label=samples)) +
theme(legend.position="none")
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'dlo' in selecting a method for function 'pcaPlot': object 'qc_filt' not found
> pcp2 <-pcaPlot(qc_filt) + geom_text_repel(aes(label=samples))
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'dlo' in selecting a method for function 'pcaPlot': object 'qc_filt' not found
> pcp2 <-pcaPlot(qc_filt) + geom_text_repel(aes(label=samples)))
Error: unexpected ')' in "pcp2 <-pcaPlot(qc_filt) + geom_text_repel(aes(label=samples)))"
> pcp2 <-pcaPlot(qc_filt) + geom_text_repel(aes(label=samples))))
Error: unexpected ')' in "pcp2 <-pcaPlot(qc_filt) + geom_text_repel(aes(label=samples)))"
> pcp2 <-pcaPlot(qc_filt) + geom_text_repel(aes(label=samples))
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'dlo' in selecting a method for function 'pcaPlot': object 'qc_filt' not found
> loopMetrics(FullR1_mango)
D4_DnmtWT_rep1.filt.intra D4_DnmtWT_rep2.filt.intra
unique 268650 276181
D4_DnmtTKO_rep1.filt.intra D4_DnmtTKO_rep2.filt.intra
unique 251928 257501
>
> client_loop: send disconnect: Broken pipe
(base) jra@greenberg14:~/Desktop$ ijm
ssh: connect to host epipax.ijm.univ-paris-diderot.priv port 22: Operation timed out
'''
#Information on file formats:
#https://genome.ucsc.edu/goldenPath/help/interact.html
#"interaction between two regions"
# string chrom; "Chromosome (or contig, scaffold, etc.). For interchromosomal, use 2 records"
# uint chromStart; "Start position of lower region. For interchromosomal, set to chromStart of this region"
# uint chromEnd; "End position of upper region. For interchromosomal, set to chromEnd of this region"
# string name; "Name of item, for display. Usually 'sourceName/targetName/exp' or empty"
# uint score; "Score (0-1000)"
# double value; "Strength of interaction or other data value. Typically basis for score"
# string exp; "Experiment name (metadata for filtering). Use . if not applicable"
# string color; "Item color. Specified as r,g,b or hexadecimal #RRGGBB or html color name, as in //www.w3.org/TR/css3-color/#html4. Use 0 and spectrum setting to shade by score"
# string sourceChrom; "Chromosome of source region (directional) or lower region. For non-directional interchromosomal, chrom of this region."
# uint sourceStart; "Start position in chromosome of source/lower/this region"
# uint sourceEnd; "End position in chromosome of source/lower/this region"
# string sourceName; "Identifier of source/lower/this region"
# string sourceStrand; "Orientation of source/lower/this region: + or -. Use . if not applicable"
# string targetChrom; "Chromosome of target region (directional) or upper region. For non-directional interchromosomal, chrom of other region"
# uint targetStart; "Start position in chromosome of target/upper/this region"
# uint targetEnd; "End position in chromosome of target/upper/this region"
# string targetName; "Identifier of target/upper/this region"
# string targetStrand; "Orientation of target/upper/this region: + or -. Use . if not applicable"