Alessandro Aiezza aaiezza
aaiezza
/ plotNorm.R
Created
June 27, 2017 14:15
ggplot2 plotting function for a Normal Distribution with lightly shaded and labeled standard deviations from the mean. User may also give lower and upper bounds, which adds shading under the curve between those points and a label with the area under the curve. (Made to accommodate for Mathematical Statistics with Applications 7th Ed. - WMS 2008)
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| ## | |
| # Standard function for printing Normal Distribution in ggplot2 | |
| # # # # | |
| plotNormCurve <- function( mean = 0, sd = 1, variance = sd ^ 2, | |
| lowerBound = NULL, upperBound = NULL, | |
| sdRange = 3.5, | |
| from = mean - (sdRange * sd), | |
| to = mean + (sdRange * sd), | |
| plotTitle = 'Normal Curve', xlab = 'x', ylab = 'density' | |
| ) |
aaiezza
/ RNA-Seq_plotUtils.R
Created
June 29, 2017 17:06
Miscellaneous functions used for plotting gene data.
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| #!/usr/bin/Rscript | |
| suppressMessages( library( calibrate ) ) | |
| suppressMessages( library( ggplot2 ) ) | |
| suppressMessages( library( ggrepel ) ) | |
| suppressMessages( library( ggdendro ) ) | |
| suppressMessages( library( dendextend ) ) | |
| suppressMessages( require( htmlwidgets ) ) | |
| suppressMessages( require( gridExtra ) ) | |
| suppressMessages( require( plotly ) ) |
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| #!/usr/bin/Rscript | |
| ## Properties | |
| FRM_GENE_FILE <- 'frm_gene_exp.diff.txt' | |
| FAV_COLS <- c( 'gene', 'sample_1', 'sample_2', 'value_1', 'value_2', 'log2(fold_change)', 'q_value' ) | |
| GENE_ID_FILTER <- '^((Mir([\\d]|let)+.*)|---|LOC\\d+|(.*Rik.*))$' | |
| HEATMAPS_DIR <- 'heatmaps' | |
| VOLCANO_WIDGET_DIR <- 'interactiveVolcanoPlots' | |
| ## Package Dependencies |
aaiezza
/ randomTools.R
Created
June 29, 2017 17:15
Random R functions. Most notably helpful is the Logger function.
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| #!/usr/bin/Rscript | |
| options( width = 120, warn = -1 ) | |
| # # # # | |
| # # Just some random R functions that are helpful # # | |
| # Override defaults of functions | |
| # gsub <- function( pattern, replacement, x, ignore.case = FALSE, perl = TRUE, fixed = FALSE, useBytes = FALSE ) | |
| # { | |
| # return( gsub(pattern, replacement, x, ignore.case = ignore.case, perl = perl, fixed = fixed, useBytes = useBytes) ); |
aaiezza
/ RNA-Seq_enrichmentAnalysis.R
Last active
February 24, 2021 21:53
Functions for performing and analyzing RNA-Seq Enrichment Analysis from multiple tools. Notably DAVID, Homer, and GeneTrail2.
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| #!/usr/bin/Rscript | |
| suppressMessages( source( '/cvri/Rutils/randomTools.R' ) ) | |
| ## | |
| # Analyze the results of HOMER after it runs | |
| # | |
| analyzeHomerEnrichment <- function( | |
| dir = 'goi', toFiles = FALSE, | |
| n = 5 ) |
aaiezza
/ RNA-Seq_xlsxWriter.R
Created
June 29, 2017 17:18
Wrapper functions for creating RNA-Seq differential expression analysis reports in Excel spreadsheets.
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| #!/usr/bin/Rscript | |
| suppressMessages( require( stringr ) ) | |
| options( java.parameters = "-Xmx32g" ) | |
| suppressMessages( require( rJava ) ) | |
| .joptions( java.parameters = "-Xmx32g" ) | |
| .jinit() |
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| require( zoo ) | |
| require( iterpc ) | |
| # Could be retreived from anywhere of course… | |
| nucleotideSequence <- sample( c('A','T','C','G'), 1000, replace=TRUE, prob=c(.1,.1,.4,.4) ) | |
| windowWidth <- 3 | |
| kmers <- rollapply( nucleotideSequence, width = windowWidth, by = 1, paste, collapse='' ) | |
| possibleKmers <- apply( getall( iterpc(4, 3, c('A','T','C','G'), replace = TRUE) ), 1, paste, collapse = '' ) |
aaiezza
/ debtSnowball.R
Last active
October 25, 2020 15:54
Function for determining how long an optimal Debt Snowball will take to pay off. Takes only current principals and interest rates. Does not take minimum payments or account for compounding.
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| loanData <- data.frame( | |
| description = c( | |
| '1-03 Direct Loan - Unsubsidized', | |
| '1-02 Direct Loan - Subsidized', | |
| 'Direct Unsubsidized Stafford', | |
| 'Direct Unsubsidized Stafford', | |
| '1-01 Direct Loan - Unsubsidized', | |
| 'Direct Unsubsidized Stafford', | |
| 'Direct Subsidized Stafford', | |
| 'Direct Unsubsidized Stafford', |
aaiezza
/ findActionsWithType.jq
Last active
June 19, 2018 18:19
Retrieve embedded actions with a "type" key
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| "type" as $filter | | |
| ._embedded | to_entries | |
| | map({(if (.value | has($filter)) then .key else empty end): .value|keys}) | |
| | add | |
| ## Sample command: | |
| # curl --silent https://api.financialwellness.com/task/tasklist/index | jq -Cf findActionsWithType.jq |
aaiezza
/ currentversion.sh
Last active
April 20, 2020 13:06
Maven Project | Bump Major, Minor, or Patch Sematic Version
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| currentversion() { | |
| # If xpath is on your machine (macos will I believe), | |
| # and the project's version is in the path `project.version`, | |
| # then it is nice to use this because it is faster. | |
| # xpath ./pom.xml 'project/version/text()' 2>/dev/null | |
| # Otherwise: | |
| mvn help:evaluate -Dexpression=project.version -q -DforceStdout | |
| } |
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