mirror of
https://github.com/KevinMidboe/linguist.git
synced 2025-12-08 20:38:47 +00:00
Arfon Smith
@@ -1584,6 +1584,8 @@ R:
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aliases:
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- R
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primary_extension: .r
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aliases:
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- Rscript
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extensions:
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- .R
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- .rsx
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@@ -649,6 +649,9 @@
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"Perl": [
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"ack"
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],
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"R": [
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"expr-dist"
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],
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"Ruby": [
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"Appraisals",
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"Capfile",
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@@ -688,8 +691,8 @@
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".gemrc"
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]
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},
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"tokens_total": 591725,
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"languages_total": 719,
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"tokens_total": 592149,
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"languages_total": 720,
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"tokens": {
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"ABAP": {
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"*/**": 1,
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@@ -52298,39 +52301,39 @@
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},
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"R": {
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"df.residual.mira": 1,
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"<": 24,
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"-": 28,
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"function": 14,
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"(": 163,
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"<": 46,
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"-": 51,
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"function": 18,
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"(": 219,
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"object": 12,
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"...": 4,
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")": 162,
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"{": 35,
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")": 220,
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"{": 46,
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"fit": 2,
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"analyses": 1,
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"[": 13,
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"]": 13,
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"[": 23,
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"]": 24,
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"return": 8,
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"df.residual": 2,
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"}": 35,
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"}": 46,
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"df.residual.lme": 1,
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"fixDF": 1,
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"df.residual.mer": 1,
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"sum": 1,
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"object@dims": 1,
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"*": 2,
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"c": 9,
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"+": 3,
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"c": 11,
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"+": 4,
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"df.residual.default": 1,
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"q": 2,
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"q": 3,
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"df": 3,
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"if": 13,
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"is.null": 2,
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"if": 19,
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"is.null": 8,
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"mk": 2,
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"try": 3,
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"coef": 1,
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"silent": 3,
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"TRUE": 12,
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"TRUE": 14,
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"mn": 2,
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"f": 9,
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"fitted": 1,
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@@ -52345,15 +52348,75 @@
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"length": 3,
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"k": 3,
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"max": 1,
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"SHEBANG#!Rscript": 1,
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"SHEBANG#!Rscript": 2,
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"#": 45,
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"MedianNorm": 2,
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"data": 11,
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"geomeans": 3,
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"<->": 1,
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"exp": 1,
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"rowMeans": 1,
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"log": 5,
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"apply": 2,
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"2": 1,
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"cnts": 2,
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"median": 1,
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"library": 1,
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"print_usage": 2,
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"file": 4,
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"stderr": 1,
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"cat": 1,
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"spec": 2,
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"matrix": 3,
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"byrow": 3,
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"ncol": 3,
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"opt": 23,
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"getopt": 1,
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"help": 1,
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"stdout": 1,
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"status": 1,
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"height": 7,
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"out": 4,
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"res": 6,
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"width": 7,
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"ylim": 7,
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"read.table": 1,
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"header": 1,
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"sep": 4,
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"quote": 1,
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"nsamp": 8,
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"dim": 1,
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"outfile": 4,
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"sprintf": 2,
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"png": 2,
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"h": 12,
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"hist": 4,
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"plot": 7,
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"FALSE": 9,
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"mids": 4,
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"density": 4,
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"type": 3,
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"col": 4,
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"rainbow": 4,
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"main": 2,
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"xlab": 2,
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"ylab": 2,
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"for": 3,
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"i": 6,
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"in": 8,
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"lines": 6,
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"devnum": 2,
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"dev.off": 2,
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"size.factors": 2,
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"data.matrix": 1,
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"data.norm": 3,
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"t": 1,
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"x": 3,
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"/": 1,
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"ParseDates": 2,
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"lines": 4,
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"dates": 3,
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"matrix": 2,
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"unlist": 2,
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"strsplit": 3,
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"ncol": 2,
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"byrow": 2,
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"days": 2,
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"times": 2,
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"hours": 2,
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@@ -52374,7 +52437,6 @@
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"ggplot": 1,
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"aes": 2,
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"y": 1,
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"x": 1,
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"geom_point": 1,
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"size": 1,
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"Freq": 1,
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@@ -52382,12 +52444,8 @@
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"range": 1,
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"ggsave": 1,
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"filename": 1,
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"plot": 1,
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"width": 1,
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"height": 1,
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"hello": 2,
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"print": 1,
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"#": 42,
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"module": 25,
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"code": 19,
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"available": 1,
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@@ -52409,7 +52467,6 @@
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"even": 1,
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"attach": 11,
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"is": 7,
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"FALSE": 5,
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"optionally": 1,
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"attached": 2,
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"to": 8,
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@@ -52419,7 +52476,6 @@
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"defaults": 1,
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".": 5,
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"However": 1,
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"in": 6,
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"interactive": 2,
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"invoked": 1,
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"directly": 1,
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@@ -52467,7 +52523,6 @@
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"first.": 1,
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"That": 1,
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"local": 3,
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"file": 1,
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"./a.r": 1,
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"will": 2,
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"loaded.": 1,
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@@ -52537,7 +52592,6 @@
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"parent": 9,
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".BaseNamespaceEnv": 1,
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"paste": 3,
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"sep": 3,
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"source": 2,
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"chdir": 1,
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"envir": 5,
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@@ -52590,7 +52644,6 @@
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"Reloading": 1,
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"primarily": 1,
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"useful": 1,
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"for": 1,
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"testing": 1,
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"during": 1,
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"module_ref": 3,
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@@ -52612,8 +52665,7 @@
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"pts": 1,
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"spsample": 1,
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"polyg": 1,
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"numpoints": 1,
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"type": 1
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"numpoints": 1
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},
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"Racket": {
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";": 3,
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@@ -63056,7 +63108,7 @@
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"Protocol Buffer": 63,
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"PureScript": 1652,
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"Python": 5715,
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"R": 1243,
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"R": 1667,
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"Racket": 331,
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"Ragel in Ruby Host": 593,
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"RDoc": 279,
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@@ -63236,7 +63288,7 @@
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"Protocol Buffer": 1,
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"PureScript": 4,
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"Python": 7,
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"R": 5,
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"R": 6,
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"Racket": 2,
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"Ragel in Ruby Host": 3,
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"RDoc": 1,
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@@ -63287,5 +63339,5 @@
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"YAML": 2,
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"Zephir": 2
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},
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"md5": "58816c8da227d1157f624a68c2f3ab55"
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"md5": "fa38e2b617caaf230146a7adab264419"
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}
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101
samples/R/filenames/expr-dist
Executable file
101
samples/R/filenames/expr-dist
Executable file
@@ -0,0 +1,101 @@
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#!/usr/bin/env Rscript
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# Copyright (c) 2013 Daniel S. Standage, released under MIT license
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#
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# expr-dist: plot distributions of expression values before and after
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# normalization; visually confirm that normalization worked
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# as expected
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#
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# Program input is a matrix of expression values, each row corresponding to a
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# molecule (gene, transcript, etc) and each row corresponding to that molecule's
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# expression level or abundance. The program expects the rows and columns to be
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# named, and was tested primarily on output produced by the
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# 'rsem-generate-data-matrix' script distributed with the RSEM package.
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#
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# The program plots the distributions of the logged expression values by sample
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# as provided, then normalizes the values, and finally plots the distribution of
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# the logged normalized expression values by sample. The expectation is that all
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# samples' distributions will have a similar shape but different medians prior
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# to normalization, and that post normalization they will all have an identical
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# median to facilitate cross-sample comparison.
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# MedianNorm function borrowed from the EBSeq library version 1.1.6
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# See http://www.bioconductor.org/packages/devel/bioc/html/EBSeq.html
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MedianNorm <- function(data)
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{
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geomeans <- exp( rowMeans(log(data)) )
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apply(data, 2, function(cnts) median((cnts/geomeans)[geomeans > 0]))
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}
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library("getopt")
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print_usage <- function(file=stderr())
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{
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cat("
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expr-dist: see source code for full description
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Usage: expr-dist [options] < expr-matrix.txt
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Options:
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-h|--help: print this help message and exit
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-o|--out: STRING prefix for output files; default is 'expr-dist'
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-r|--res: INT resolution (dpi) of generated graphics; default is 150
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-t|--height: INT height (pixels) of generated graphics; default is 1200
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-w|--width: INT width (pixels) of generated graphics; default is 1200
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-y|--ylim: REAL the visible range of the Y axis depends on the first
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distribution plotted; if other distributions are getting
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cut off, use this setting to override the default\n\n")
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}
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spec <- matrix( c("help", 'h', 0, "logical",
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"out", 'o', 1, "character",
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"res", 'r', 1, "integer",
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"height", 't', 1, "integer",
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"width", 'w', 1, "integer",
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"ylim", 'y', 1, "double"),
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byrow=TRUE, ncol=4)
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opt <- getopt(spec)
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if(!is.null(opt$help))
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{
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print_usage(file=stdout())
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q(status=1)
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}
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if(is.null(opt$height)) { opt$height <- 1200 }
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if(is.null(opt$out)) { opt$out <- "expr-dist" }
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if(is.null(opt$res)) { opt$res <- 150 }
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if(is.null(opt$width)) { opt$width <- 1200 }
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if(!is.null(opt$ylim)) { opt$ylim <- c(0, opt$ylim) }
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# Load data, determine number of samples
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data <- read.table(file("stdin"), header=TRUE, sep="\t", quote="")
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nsamp <- dim(data)[2] - 1
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data <- data[,1:nsamp+1]
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# Plot distribution of expression values before normalization
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outfile <- sprintf("%s-median.png", opt$out)
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png(outfile, height=opt$height, width=opt$width, res=opt$res)
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h <- hist(log(data[,1]), plot=FALSE)
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plot(h$mids, h$density, type="l", col=rainbow(nsamp)[1], main="",
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xlab="Log expression value", ylab="Proportion of molecules", ylim=opt$ylim)
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for(i in 2:nsamp)
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{
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h <- hist(log(data[,i]), plot=FALSE)
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lines(h$mids, h$density, col=rainbow(nsamp)[i])
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}
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devnum <- dev.off()
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# Normalize by median
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size.factors <- MedianNorm(data.matrix(data))
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data.norm <- t(apply(data, 1, function(x){ x / size.factors }))
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# Plot distribution of normalized expression values
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outfile <- sprintf("%s-median-norm.png", opt$out)
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png(outfile, height=opt$height, width=opt$width, res=opt$res)
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h <- hist(log(data.norm[,1]), plot=FALSE)
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plot(h$mids, h$density, type="l", col=rainbow(nsamp)[1], main="",
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xlab="Log normalized expression value", ylab="Proportion of molecules",
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ylim=opt$ylim)
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for(i in 2:nsamp)
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{
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h <- hist(log(data.norm[,i]), plot=FALSE)
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lines(h$mids, h$density, col=rainbow(nsamp)[i])
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}
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devnum <- dev.off()
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Reference in New Issue
Block a user