library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(tidyverse)
## Warning: package 'ggplot2' was built under R version 4.3.2
## Warning: package 'tidyr' was built under R version 4.3.2
## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ forcats 1.0.0.9000 ✔ readr 2.1.5
## ✔ ggplot2 3.5.1 ✔ stringr 1.5.1
## ✔ lubridate 1.9.3 ✔ tibble 3.2.1
## ✔ purrr 1.0.2 ✔ tidyr 1.3.1
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
library(variancePartition)
## Loading required package: limma
## Loading required package: BiocParallel
## Warning: package 'BiocParallel' was built under R version 4.3.1
##
## Attaching package: 'variancePartition'
##
## The following object is masked from 'package:limma':
##
## topTable
library(RColorBrewer)
metadata.updated <- read.csv("~/Desktop/Dilpreet.JTC.Analysis/JTC.Input.Samples/DEPanalysis/metadata.JTC_InputSample_Metadata.updated.csv", row.names = 1)
metadata.updated
## Input.JTC_Samples Group
## JTC1 JTC1 Control
## JTC2 JTC2 Control
## JTC3 JTC3 Control
## X73.1 X73.1 N-Terminal
## X73.2 X73.2 N-Terminal
## X73.3 X73.3 N-Terminal
## X74.1 X74.1 C-Terminal
## X74.2 X74.2 C-Terminal
## X74.3 X74.3 C-Terminal
## X77.1 X77.1 C-Terminal.del.PDZ
## X77.2 X77.2 C-Terminal.del.PDZ
## X77.3 X77.3 C-Terminal.del.PDZ
SRIVAST_JTC_IP_normalized.quantile <- readRDS("~/Desktop/Dilpreet.JTC.Analysis/JTC.Input.Samples/DEPanalysis/SRIVAST_JTC_IP_normalized.quantile.rds")
cleanDat <- SRIVAST_JTC_IP_normalized.quantile
numericMeta <- metadata.updated
condition <- metadata.updated$Group
Grouping <- metadata.updated$Group
source("/Users/usri/Desktop/Screen/parANOVA.dex.R")
ANOVAout <- parANOVA.dex()
## - Grouping values have '-'; replacing with '.'...
## - parallelThreads variable not set. Running with 2 threads only.
## - Network color assignment vector not supplied or not of length in rows of cleanDat; will not be included in output table and data frame.
## - twoGroupCorrMethod variable not set to a correction method for p.adjust when only 2 groups of samples specified in Grouping. Using Benjamini Hochberg 'BH' FDR.
## - fallbackIfSmallTukeyP variable not set. Using recommended Bonferroni t-test FDR for unreliable Tukey p values <10^-8.5
##
## Attaching package: 'foreach'
##
## The following objects are masked from 'package:purrr':
##
## accumulate, when
##
## ...Tukey p<10^-8.5 Fallback calculations using Bonferroni corrected T test: 2 [0.013%]
labelTop <- 15
FCmin= 3
flip = -3
signifP=0.05
plotVolc()
## - No comparison p value columns selected in selectComps. Using ALL comparisons.
## - selectComps may not reference valid integer p value column indexes of ANOVAout (or CORout).
## Output will be for all comparisons or correlation(s).
## - useNETcolors not set or not TRUE/FALSE. NETcolors not found in ANOVAout, so 3 color volcano(es) will be drawn.
## - Variable outputfigs not specified. Saving volcano plots to /Users/usri/Desktop/Dilpreet.JTC.Analysis/JTC.4fold.Reanalysis/Oct30.24 .
##
## ...Thresholds:
## [x] Applying a 300% minimum fold change threshold at + and - x=2 .
## [y] with minimum significance cutoff p < 0.05, equivalent to -log10(p) y=1.3 .
##
## Processing ANOVA column 3 (C.Terminal.del.PDZ vs C.Terminal) for volcano ...
## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## Warning: package 'ggrepel' was built under R version 4.3.3
## Processing ANOVA column 4 (Control vs C.Terminal) for volcano ...
## Processing ANOVA column 5 (N.Terminal vs C.Terminal) for volcano ...
## Processing ANOVA column 6 (Control vs C.Terminal.del.PDZ) for volcano ...
## Processing ANOVA column 7 (N.Terminal vs C.Terminal.del.PDZ) for volcano ...
## Processing ANOVA column 8 (N.Terminal vs Control) for volcano ...
## Generating PDF volcano for ANOVAout column 3 (C.Terminal.del.PDZ vs C.Terminal) ...
## Generating PDF volcano for ANOVAout column 4 (Control vs C.Terminal) ...
## Generating PDF volcano for ANOVAout column 5 (N.Terminal vs C.Terminal) ...
## Generating PDF volcano for ANOVAout column 6 (Control vs C.Terminal.del.PDZ) ...
## Generating PDF volcano for ANOVAout column 7 (N.Terminal vs C.Terminal.del.PDZ) ...
## Generating PDF volcano for ANOVAout column 8 (N.Terminal vs Control) ...
## Generating HTML volcano for ANOVAout column 3 (C.Terminal.del.PDZ vs C.Terminal) ...
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Generating HTML volcano for ANOVAout column 4 (Control vs C.Terminal) ...
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Generating HTML volcano for ANOVAout column 5 (N.Terminal vs C.Terminal) ...
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Generating HTML volcano for ANOVAout column 6 (Control vs C.Terminal.del.PDZ) ...
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Generating HTML volcano for ANOVAout column 7 (N.Terminal vs C.Terminal.del.PDZ) ...
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Generating HTML volcano for ANOVAout column 8 (N.Terminal vs Control) ...
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
library(dplyr)
library(tidyverse)
library(variancePartition)
library(RColorBrewer)
metadata.updated <- read.csv("~/Desktop/Dilpreet.JTC.Analysis/JTC.Input.Samples/DEPanalysis/metadata.JTC_InputSample_Metadata.updated.csv", row.names = 1)
metadata.updated
SRIVAST_JTC_IP_normalized.quantile <- readRDS("~/Desktop/Dilpreet.JTC.Analysis/JTC.Input.Samples/DEPanalysis/SRIVAST_JTC_IP_normalized.quantile.rds")
cleanDat <- SRIVAST_JTC_IP_normalized.quantile
numericMeta <- metadata.updated
condition <- metadata.updated$Group
Grouping <- metadata.updated$Group
source("/Users/usri/Desktop/Screen/parANOVA.dex.R")
numericMeta <- metadata.updated
condition <- metadata.updated$Group
Grouping <- metadata.updated$Group
source("/Users/usri/Desktop/parANOVA.dex.R")
numericMeta <- metadata.updated
condition <- metadata.updated$Group
Grouping <- metadata.updated$Group
source("/Users/us74/Desktop/parANOVA.dex.R")
ANOVAout <- parANOVA.dex()
labelTop <- 15
FCmin= 3
flip = -3
signifP=0.05
plotVolc()