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Continuing to complete to-do tasks for the RRP6-NAB3 manuscript; see …
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…time_FHCC.xlsx and emails
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Kris Alavattam committed Jul 4, 2023
1 parent 85632bc commit 16b564f
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248 changes: 178 additions & 70 deletions results/2023-0215/rough-draft_coverage-tracks.sh
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153 changes: 91 additions & 62 deletions results/2023-0215/rough-draft_draw_scatter-plots.R
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Original file line number Diff line number Diff line change
Expand Up @@ -496,8 +496,8 @@ p_mRNA_AS <- "rds_mRNA-AS"
p_ncRNAcm <- "rds_ncRNA-collapsed"
p_R64_etc <- "rds_coding-non-pa-ncRNA"

# mRNA features
load_mRNA_N_Q_r6n <- FALSE #ARGUMENT
# mRNA features ------------------------------------------
load_mRNA_N_Q_r6n <- TRUE #ARGUMENT
if(base::isTRUE(load_mRNA_N_Q_r6n)) {
mRNA_N_Q_r6n <- readRDS(paste(
p_RDS,
Expand All @@ -507,7 +507,7 @@ if(base::isTRUE(load_mRNA_N_Q_r6n)) {
))
}

load_mRNA_SS_Q_r6n <- FALSE #ARGUMENT
load_mRNA_SS_Q_r6n <- TRUE #ARGUMENT
if(base::isTRUE(load_mRNA_SS_Q_r6n)) {
mRNA_SS_Q_r6n <- readRDS(paste(
p_RDS,
Expand Down Expand Up @@ -548,7 +548,7 @@ if(base::isTRUE(load_mRNA_SS_Q_n3d)) {
}


# collapsed, merged pa-ncRNA features ----------
# collapsed, merged pa-ncRNA features --------------------
load_ncRNAcm_N_Q_r6n <- FALSE #ARGUMENT
if(base::isTRUE(load_ncRNAcm_N_Q_r6n)) {
ncRNAcm_N_Q_r6n <- readRDS(paste(
Expand Down Expand Up @@ -600,8 +600,8 @@ if(base::isTRUE(load_ncRNAcm_SS_Q_n3d)) {
}


# antisense mRNA features ----------------------
`load_mRNA-AS_N_Q_r6n` <- FALSE #ARGUMENT
# antisense mRNA features --------------------------------
`load_mRNA-AS_N_Q_r6n` <- TRUE #ARGUMENT
if(base::isTRUE(`load_mRNA-AS_N_Q_r6n`)) {
`mRNA-AS_N_Q_r6n` <- readRDS(paste(
p_RDS,
Expand All @@ -612,7 +612,7 @@ if(base::isTRUE(`load_mRNA-AS_N_Q_r6n`)) {

}

`load_mRNA-AS_SS_Q_r6n` <- FALSE #ARGUMENT
`load_mRNA-AS_SS_Q_r6n` <- TRUE #ARGUMENT
if(base::isTRUE(`load_mRNA-AS_SS_Q_r6n`)) {
`mRNA-AS_SS_Q_r6n` <- readRDS(paste(
p_RDS,
Expand Down Expand Up @@ -655,7 +655,7 @@ if(base::isTRUE(`load_mRNA-AS_SS_Q_n3d`)) {
}


# R64 coding, noncoding, etc. features ---------
# R64 coding, noncoding, etc. features ------------------
`load_R64-etc_N_Q_r6n` <- FALSE #ARGUMENT
if(base::isTRUE(`load_R64-etc_N_Q_r6n`)) {
`R64-etc_N_Q_r6n` <- readRDS(paste(
Expand Down Expand Up @@ -686,7 +686,7 @@ if(base::isTRUE(`load_R64-etc_SS_G1_r6n`)) {
))
}

`load_R64-etc_N_Q_n3d` <- TRUE #ARGUMENT
`load_R64-etc_N_Q_n3d` <- FALSE #ARGUMENT
if(base::isTRUE(`load_R64-etc_N_Q_n3d`)) {
`R64-etc_N_Q_n3d` <- readRDS(paste(
p_RDS,
Expand Down Expand Up @@ -721,7 +721,43 @@ rm(list = ls(pattern = "p_"))


# Draw scatter plots and do linear modeling ----------------------------------
# Look at SS Q rrp6∆ ~ N Q rrp6∆ (SS_Q_r6n ~ N_Q_r6n) for mRNA
# Fig. 3 -------------------------------------------------
# Fig. 3B: Look at SS_G1_r6n ~ SS_Q_r6n for mRNA
#+ i.e., mRNA_SS_G1_r6n ~ mRNA_SS_Q_r6n
run <- FALSE
if(base::isTRUE(run)) {
`mRNA_SS-G1-r6n_SS-Q-r6n` <- model_plot_scatter_log2FC(
x = mRNA_SS_Q_r6n$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
y = mRNA_SS_G1_r6n$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
color = "#481A6C33",
xlab = "Q log2(FC) steady state rrp6n/WT",
ylab = "G1 log2(FC) steady state rrp6n/WT",
x_low = -7,
x_high = 7,
y_low = -7,
y_high = 7
)
}

# Fig. 3B: Look at SS_G1_r6n ~ SS_Q_r6n for pa-ncRNA
#+ i.e., ncRNAcm_SS_G1_r6n ~ ncRNAcm_SS_Q_r6n
run <- FALSE
if(base::isTRUE(run)) {
`ncRNAcm_SS-G1-r6n_SS-Q-r6n` <- model_plot_scatter_log2FC(
x = ncRNAcm_SS_Q_r6n$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
y = ncRNAcm_SS_G1_r6n$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
color = "#481A6C33",
xlab = "Q log2(FC) steady state rrp6n/WT",
ylab = "G1 log2(FC) steady state rrp6n/WT",
x_low = -7,
x_high = 7,
y_low = -7,
y_high = 7
)
}

# Fig. 3D: Look at SS Q rrp6∆ ~ N Q rrp6∆ (SS_Q_r6n ~ N_Q_r6n) for mRNA
#+ i.e., mRNA_SS_Q_r6n ~ mRNA_N_Q_r6n
run <- FALSE
if(base::isTRUE(run)) {
`mRNA_SS-Q-r6n_N-Q-r6n` <- model_plot_scatter_log2FC(
Expand All @@ -737,7 +773,8 @@ if(base::isTRUE(run)) {
)
}

# Look at SS Q rrp6∆ ~ N Q rrp6∆ (SS_Q_r6n ~ N_Q_r6n) for pa-ncRNA
# Fig. 3D: Look at SS Q rrp6∆ ~ N Q rrp6∆ (SS_Q_r6n ~ N_Q_r6n) for pa-ncRNA
#+ i.e., ncRNAcm_SS_Q_r6n ~ ncRNAcm_N_Q_r6n
run <- FALSE
if(base::isTRUE(run)) {
`ncRNAcm_SS-Q-r6n_N-Q-r6n` <- model_plot_scatter_log2FC(
Expand All @@ -753,7 +790,9 @@ if(base::isTRUE(run)) {
)
}

# Look at SS Q rrp6∆ ~ N Q nab3d for mRNA
# Fig. 4 -------------------------------------------------
# Fig. 4B: Look at SS Q rrp6∆ ~ N Q nab3d for mRNA
#+ i.e., mRNA_SS_Q_r6n ~ mRNA_N_Q_n3d
run <- FALSE
if(base::isTRUE(run)) {
`mRNA_SS-Q-r6n_N-Q-n3d` <- model_plot_scatter_log2FC(
Expand All @@ -769,7 +808,8 @@ if(base::isTRUE(run)) {
)
}

# Look at SS Q rrp6∆ ~ N Q nab3d for pa-ncRNA
# Fig. 4B: Look at SS Q rrp6∆ ~ N Q nab3d for pa-ncRNA
#+ i.e., ncRNAcm_SS_Q_r6n ~ ncRNAcm_N_Q_n3d
run <- FALSE
if(base::isTRUE(run)) {
`ncRNAcm_SS-Q-r6n_N-Q-n3d` <- model_plot_scatter_log2FC(
Expand All @@ -785,7 +825,8 @@ if(base::isTRUE(run)) {
)
}

# Look at SS Q rrp6∆ ~ SS Q nab3d for mRNA
# Fig. 4_: Look at SS Q rrp6∆ ~ SS Q nab3d for mRNA
#+ i.e., mRNA_SS_Q_r6n ~ mRNA_SS_Q_n3d
run <- FALSE
if(base::isTRUE(run)) {
`mRNA_SS-Q-r6n_SS-Q-n3d` <- model_plot_scatter_log2FC(
Expand All @@ -801,7 +842,8 @@ if(base::isTRUE(run)) {
)
}

# Look at SS Q rrp6∆ ~ SS Q nab3d for pa-ncRNA
# Fig. 4_: Look at SS Q rrp6∆ ~ SS Q nab3d for pa-ncRNA
#+ i.e., ncRNAcm_SS_Q_r6n ~ ncRNAcm_SS_Q_n3d
run <- FALSE
if(base::isTRUE(run)) {
`ncRNAcm_SS-Q-r6n_SS-Q-n3d` <- model_plot_scatter_log2FC(
Expand All @@ -817,46 +859,30 @@ if(base::isTRUE(run)) {
)
}


# Look at SS_G1_r6n ~ SS_Q_r6n for mRNA
# Fig. 4C: Look at N Q Nab3-AID mRNA ~ N Q Nab3-AID mRNA antisense
#+ i.e., mRNA_N_Q_n3d ~ `mRNA-AS_N_Q_n3d`
run <- FALSE
if(base::isTRUE(run)) {
`mRNA_SS-G1-r6n_SS-Q-r6n` <- model_plot_scatter_log2FC(
x = mRNA_SS_Q_r6n$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
y = mRNA_SS_G1_r6n$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
color = "#481A6C33",
xlab = "Q log2(FC) steady state rrp6n/WT",
ylab = "G1 log2(FC) steady state rrp6n/WT",
x_low = -7,
x_high = 7,
y_low = -7,
y_high = 7
)
}

# Look at SS_G1_r6n ~ SS_Q_r6n for pa-ncRNA
run <- FALSE
if(base::isTRUE(run)) {
`ncRNAcm_SS-G1-r6n_SS-Q-r6n` <- model_plot_scatter_log2FC(
x = ncRNAcm_SS_Q_r6n$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
y = ncRNAcm_SS_G1_r6n$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
color = "#481A6C33",
xlab = "Q log2(FC) steady state rrp6n/WT",
ylab = "G1 log2(FC) steady state rrp6n/WT",
x_low = -7,
x_high = 7,
y_low = -7,
y_high = 7
`mRNA-mRNA-AS_N-Q-n3d` <- model_plot_scatter_log2FC(
x = `mRNA-AS_N_Q_n3d`$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
y = mRNA_N_Q_n3d$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
color = "#3A538833",
xlab = "log2(FC) mRNA antisense",
ylab = "log2(FC) mRNA",
x_low = -9,
x_high = 9,
y_low = -9,
y_high = 9
)
}

# Look at N Q Nab3-AID mRNA ~ N Q Nab3-AID mRNA antisense
#+ (N_Q_n3d ~ N_Q_n3d_AS)
run <- FALSE
# Fig. 4_: Look at N Q Rrp6∆ mRNA ~ N Q Rrp6∆ mRNA antisense
#+ i.e., mRNA_N_Q_r6n ~ `mRNA-AS_N_Q_r6n`
run <- TRUE
if(base::isTRUE(run)) {
`mRNA-mRNA-AS_N-Q-n3d` <- model_plot_scatter_log2FC(
x = mRNA_N_Q_n3d$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
y = `mRNA-AS_N_Q_n3d`$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
`mRNA-mRNA-AS_N-Q-r6n` <- model_plot_scatter_log2FC(
x = `mRNA-AS_N_Q_r6n`$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
y = mRNA_N_Q_r6n$`09_lfc_0.58_fc_1.5`$`04_t_DGE_unshrunken`,
color = "#3A538833",
xlab = "log2(FC) mRNA antisense",
ylab = "log2(FC) mRNA",
Expand All @@ -867,7 +893,8 @@ if(base::isTRUE(run)) {
)
}

# Look at SS Q Nab3-AID ~ N Q Nab3-AID for mRNA
# Fig. 4_: Look at SS Q Nab3-AID ~ N Q Nab3-AID for mRNA
#+ i.e., mRNA_SS_Q_n3d ~ mRNA_N_Q_n3d
run <- FALSE
if(base::isTRUE(run)) {
`mRNA_SS-Q-n3d_N-Q-n3d` <- model_plot_scatter_log2FC(
Expand All @@ -883,7 +910,8 @@ if(base::isTRUE(run)) {
)
}

# Look at N SS Nab3-AID ~ N Q Nab3-AID for pa-ncRNA
# Fig. 4_: Look at SS Q Nab3-AID ~ N Q Nab3-AID for pa-ncRNA
#+ i.e., ncRNAcm_SS_Q_n3d ~ ncRNAcm_N_Q_n3d
run <- FALSE
if(base::isTRUE(run)) {
`ncRNAcm_SS-Q-n3d_N-Q-n3d` <- model_plot_scatter_log2FC(
Expand All @@ -903,55 +931,56 @@ if(base::isTRUE(run)) {
# Write out scatter-plot-etc lists as rds objects ----------------------------
run <- FALSE
if(base::isTRUE(run)) {
output_rds(`mRNA_SS-G1-r6n_SS-Q-r6n`)
output_rds(`ncRNAcm_SS-G1-r6n_SS-Q-r6n`)
output_rds(`mRNA_SS-Q-r6n_N-Q-r6n`)
output_rds(`ncRNAcm_SS-Q-r6n_N-Q-r6n`)
output_rds(`mRNA_SS-Q-r6n_N-Q-n3d`)
output_rds(`ncRNAcm_SS-Q-r6n_N-Q-n3d`)
output_rds(`mRNA_SS-Q-r6n_SS-Q-n3d`)
output_rds(`ncRNAcm_SS-Q-r6n_SS-Q-n3d`)
output_rds(`mRNA_SS-G1-r6n_SS-Q-r6n`)
output_rds(`ncRNAcm_SS-G1-r6n_SS-Q-r6n`)
output_rds(`mRNA-mRNA-AS_N-Q-n3d`)
output_rds(`mRNA-mRNA-AS_N-Q-r6n`)
output_rds(`mRNA_SS-Q-n3d_N-Q-n3d`)
output_rds(`ncRNAcm_SS-Q-n3d_N-Q-n3d`)
}


# Write out pdfs of scatter plots --------------------------------------------
run <- FALSE
if(base::isTRUE(run)) {
print_scatter(dataframe = `mRNA_SS-G1-r6n_SS-Q-r6n`)
print_scatter(dataframe = `ncRNAcm_SS-G1-r6n_SS-Q-r6n`)
print_scatter(dataframe = `mRNA_SS-Q-r6n_N-Q-r6n`)
print_scatter(dataframe = `ncRNAcm_SS-Q-r6n_N-Q-r6n`)
print_scatter(dataframe = `mRNA_SS-Q-r6n_N-Q-n3d`)
print_scatter(dataframe = `ncRNAcm_SS-Q-r6n_N-Q-n3d`)
print_scatter(dataframe = `mRNA_SS-Q-r6n_SS-Q-n3d`)
print_scatter(dataframe = `ncRNAcm_SS-Q-r6n_SS-Q-n3d`)
print_scatter(dataframe = `mRNA_SS-G1-r6n_SS-Q-r6n`)
print_scatter(dataframe = `ncRNAcm_SS-G1-r6n_SS-Q-r6n`)
print_scatter(dataframe = `mRNA-mRNA-AS_N-Q-n3d`)
print_scatter(dataframe = `mRNA-mRNA-AS_N-Q-r6n`)
print_scatter(dataframe = `mRNA_SS-Q-n3d_N-Q-n3d`)
print_scatter(dataframe = `ncRNAcm_SS-Q-n3d_N-Q-n3d`)
}

check <- FALSE
if(base::isTRUE(check)) {
`mRNA_SS-G1-r6n_SS-Q-r6n`$`05_scatter_density`
`ncRNAcm_SS-G1-r6n_SS-Q-r6n`$`05_scatter_density`
`mRNA_SS-Q-r6n_N-Q-r6n`$`05_scatter_density`
`ncRNAcm_SS-Q-r6n_N-Q-r6n`$`05_scatter_density`
`mRNA_SS-Q-r6n_N-Q-n3d`$`05_scatter_density`
`ncRNAcm_SS-Q-r6n_N-Q-n3d`$`05_scatter_density`
`mRNA_SS-Q-r6n_SS-Q-n3d`$`05_scatter_density`
`ncRNAcm_SS-Q-r6n_SS-Q-n3d`$`05_scatter_density`
`mRNA_SS-G1-r6n_SS-Q-r6n`$`05_scatter_density`
`ncRNAcm_SS-G1-r6n_SS-Q-r6n`$`05_scatter_density`
`mRNA-mRNA-AS_N-Q-n3d`$`05_scatter_density`
`mRNA-mRNA-AS_N-Q-r6n`$`05_scatter_density`
`mRNA_SS-Q-n3d_N-Q-n3d`$`05_scatter_density`
`ncRNAcm_SS-Q-n3d_N-Q-n3d`$`05_scatter_density`
}


# Custom work: Plot Nab3-AID/parent log2FC w/r/to ORF length =================
# Color rules: "If all Steady State use purple 481A6C: if all Nascent, then
#+ use blue 3A5388."

# Custom work: Fig. 5: Plot Nab3-AID/parent log2FC w/r/to ORF length =========
run <- FALSE
if(base::isTRUE(run)) {
# ...for Nab3-AID Nascent Q --------------------------
Expand Down Expand Up @@ -1321,4 +1350,4 @@ if(base::isTRUE(run)) {
title = "",
subtitle = ""
)
}
}
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