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fix(profile-plots): Fix scaling of profile plots based on individual … #133

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10 changes: 6 additions & 4 deletions R/dataProcessPlotsPTM.R
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Original file line number Diff line number Diff line change
Expand Up @@ -26,11 +26,13 @@
#' log intensities across MS runs.
#' "QCPlot" represents box plots of log intensities across channels and MS runs.
#' @param ylimUp upper limit for y-axis in the log scale.
#' FALSE(Default) for Profile Plot and QC Plot uses the upper limit as rounded
#' off maximum of log2(intensities) after normalization + 3..
#' FALSE(Default) for Profile Plot uses the maximum log2 intensity of the
#' protein of interest + 5 per plot; for QC Plot uses the maximum across all
#' proteins + 3.
#' @param ylimDown lower limit for y-axis in the log scale. FALSE(Default) for
#' Profile Plot and QC Plot uses the lower limit as floor of minimum
#' log2(intensities) after normalization - 3, or 0 if that value is negative.
#' Profile Plot uses the floor of the minimum log2 intensity of the protein of
#' interest - 3 (minimum 0) per plot; for QC Plot uses the floor of the minimum
#' across all proteins - 3, or 0 if that value is negative.
#' @param x.axis.size size of x-axis labeling for "Run" and "channel in Profile
#' Plot and QC Plot.
#' @param y.axis.size size of y-axis labels. Default is 10.
Expand Down
142 changes: 101 additions & 41 deletions R/utils_dataProcessPlots.R
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Original file line number Diff line number Diff line change
Expand Up @@ -606,20 +606,36 @@
}

## factoring for run, channel, condition should be done before loop

for (i in seq_len(nrow(plot_proteins))) {

ptm_temp = .plot.profile.tmt(ptm.list,
as.character(plot_proteins[, PROTEINNAME][i]),
ptm_name = as.character(plot_proteins[, PROTEINNAME][i])
ptm_abund = datafeature.ptm[datafeature.ptm$PROTEINNAME == ptm_name, ]$ABUNDANCE
if (plot_global) {
protein_name = as.character(plot_proteins[, GLOBALPROTEIN][i])
protein_abund = datafeature.protein[datafeature.protein$PROTEINNAME == protein_name, ]$ABUNDANCE
all_abund = c(ptm_abund, protein_abund)
} else {
all_abund = ptm_abund
}
if (!is.numeric(ylimUp)) y.limup = ceiling(max(all_abund, na.rm = TRUE) + 5)
if (!is.numeric(ylimDown)) y.limdown = max(floor(min(all_abund, na.rm = TRUE) - 3), 0)
cur_ptm.list = ptm.list
cur_ptm.list[[3]]$abundance = y.limup - 0.5
cur_ptm.list[[4]]$abundance = y.limup - 0.5

ptm_temp = .plot.profile.tmt(cur_ptm.list,
ptm_name,
y.limup, y.limdown, x.axis.size,
y.axis.size, text.size, text.angle, legend.size,
dot.size.profile, ncol.guide)
if (plot_global){
protein_temp = .plot.profile.tmt(protein.list,
as.character(
plot_proteins[, GLOBALPROTEIN][i]),
cur_protein.list = protein.list
cur_protein.list[[3]]$abundance = y.limup - 0.5
cur_protein.list[[4]]$abundance = y.limup - 0.5
protein_temp = .plot.profile.tmt(cur_protein.list,
protein_name,
y.limup, y.limdown, x.axis.size,
y.axis.size, text.size, text.angle,
y.axis.size, text.size, text.angle,
legend.size, dot.size.profile, ncol.guide)
original_profile_plots <- list(PTEMP.PTM = ptm_temp, PTEMP.PROTEIN = protein_temp)
grid.arrange(ptm_temp, protein_temp, ncol=1)
Expand All @@ -628,8 +644,8 @@
print(ptm_temp)
}
output_plots[["original_plot"]][[paste("plot",i)]] <- original_profile_plots
message(paste0("Drew the Profile plot for ",
as.character(plot_proteins[, PROTEINNAME][i]),
message(paste0("Drew the Profile plot for ",
ptm_name,
" (", i, " of ", nrow(plot_proteins), ")"))
}
# end-loop for each protein
Expand Down Expand Up @@ -661,14 +677,31 @@
}

for (i in seq_len(nrow(plot_proteins))) {

ptm_temp = .plot.profile.summary.tmt(ptm.list, as.character(
plot_proteins[, PROTEINNAME][i]), y.limup, y.limdown, x.axis.size,
y.axis.size, text.size, text.angle, legend.size,dot.size.profile,
ptm_name = as.character(plot_proteins[, PROTEINNAME][i])
ptm_abund = datafeature.ptm[datafeature.ptm$PROTEINNAME == ptm_name, ]$ABUNDANCE
if (plot_global) {
protein_name = as.character(plot_proteins[, GLOBALPROTEIN][i])
protein_abund = datafeature.protein[datafeature.protein$PROTEINNAME == protein_name, ]$ABUNDANCE
all_abund = c(ptm_abund, protein_abund)
} else {
all_abund = ptm_abund
}
if (!is.numeric(ylimUp)) y.limup = ceiling(max(all_abund, na.rm = TRUE) + 5)
if (!is.numeric(ylimDown)) y.limdown = max(floor(min(all_abund, na.rm = TRUE) - 3), 0)
cur_ptm.list = ptm.list
cur_ptm.list[[3]]$abundance = y.limup - 0.5
cur_ptm.list[[4]]$abundance = y.limup - 0.5

ptm_temp = .plot.profile.summary.tmt(cur_ptm.list, ptm_name,
y.limup, y.limdown, x.axis.size,
y.axis.size, text.size, text.angle, legend.size, dot.size.profile,
ncol.guide)
if (plot_global){
protein_temp = .plot.profile.summary.tmt(protein.list, as.character(
plot_proteins[, GLOBALPROTEIN][i]), y.limup, y.limdown, x.axis.size,
cur_protein.list = protein.list
cur_protein.list[[3]]$abundance = y.limup - 0.5
cur_protein.list[[4]]$abundance = y.limup - 0.5
protein_temp = .plot.profile.summary.tmt(cur_protein.list, protein_name,
y.limup, y.limdown, x.axis.size,
y.axis.size, text.size, text.angle, legend.size,
dot.size.profile, ncol.guide)
summary_profile_plots <- list(PTEMP.PTM = ptm_temp, PTEMP.PROTEIN = protein_temp)
Expand All @@ -678,10 +711,9 @@
print(ptm_temp)
}
output_plots[["summary_plot"]][[paste("plot",i)]] <- summary_profile_plots
message(paste("Drew the Profile plot for ",
as.character(plot_proteins[, PROTEINNAME][i]),
message(paste("Drew the Profile plot for ",
ptm_name,
"(", i, " of ", nrow(plot_proteins), ")"))

}

if (address!=FALSE & !isPlotly) {
Expand Down Expand Up @@ -1430,20 +1462,33 @@
## factoring for run, channel, condition should be done before loop

for (i in seq_len(nrow(plot_proteins))) {

ptm_temp = .plot.profile.lf(ptm.list,
as.character(
plot_proteins[, PROTEINNAME][i]),
ptm_name = as.character(plot_proteins[, PROTEINNAME][i])
ptm_abund = datafeature.ptm[datafeature.ptm$PROTEINNAME == ptm_name, ]$ABUNDANCE
if (plot_global) {
protein_name = as.character(plot_proteins[, GLOBALPROTEIN][i])
protein_abund = datafeature.protein[datafeature.protein$PROTEINNAME == protein_name, ]$ABUNDANCE
all_abund = c(ptm_abund, protein_abund)
} else {
all_abund = ptm_abund
}
if (!is.numeric(ylimUp)) y.limup = ceiling(max(all_abund, na.rm = TRUE) + 5)
if (!is.numeric(ylimDown)) y.limdown = max(floor(min(all_abund, na.rm = TRUE) - 3), 0)
cur_ptm.list = ptm.list
cur_ptm.list[[3]]$ABUNDANCE = y.limup - 1

ptm_temp = .plot.profile.lf(cur_ptm.list,
ptm_name,
y.limup, y.limdown, x.axis.size,
y.axis.size, text.size, text.angle,
y.axis.size, text.size, text.angle,
legend.size, dot.size.profile, ncol.guide)
if (plot_global) {
protein_temp = .plot.profile.lf(protein.list,
as.character(
plot_proteins[, GLOBALPROTEIN][i]),
cur_protein.list = protein.list
cur_protein.list[[3]]$ABUNDANCE = y.limup - 1
protein_temp = .plot.profile.lf(cur_protein.list,
protein_name,
y.limup, y.limdown, x.axis.size,
y.axis.size, text.size, text.angle,
legend.size, dot.size.profile,
y.axis.size, text.size, text.angle,
legend.size, dot.size.profile,
ncol.guide)
original_profile_plots <- list(PTEMP.PTM = ptm_temp, PTEMP.PROTEIN = protein_temp)
grid.arrange(ptm_temp, protein_temp, ncol=1)
Expand All @@ -1452,8 +1497,8 @@
print(ptm_temp)
}
output_plots[["original_plot"]][[paste("plot",i)]] <- original_profile_plots
message(paste0("Drew the Profile plot for ",
as.character(plot_proteins[, PROTEINNAME][i]),
message(paste0("Drew the Profile plot for ",
ptm_name,
" (", i, " of ", nrow(plot_proteins), ")"))
}
# end-loop for each protein
Expand Down Expand Up @@ -1485,16 +1530,31 @@
}

for (i in seq_len(nrow(plot_proteins))) {

ptm_temp = .plot.profile.summary.lf(ptm.list, as.character(
plot_proteins[, PROTEINNAME][i]), y.limup, y.limdown, x.axis.size,
y.axis.size, text.size, text.angle, legend.size,dot.size.profile,
ptm_name = as.character(plot_proteins[, PROTEINNAME][i])
ptm_abund = datafeature.ptm[datafeature.ptm$PROTEINNAME == ptm_name, ]$ABUNDANCE
if (plot_global) {
protein_name = as.character(plot_proteins[, GLOBALPROTEIN][i])
protein_abund = datafeature.protein[datafeature.protein$PROTEINNAME == protein_name, ]$ABUNDANCE
all_abund = c(ptm_abund, protein_abund)
} else {
all_abund = ptm_abund
}
if (!is.numeric(ylimUp)) y.limup = ceiling(max(all_abund, na.rm = TRUE) + 5)
if (!is.numeric(ylimDown)) y.limdown = max(floor(min(all_abund, na.rm = TRUE) - 3), 0)
cur_ptm.list = ptm.list
cur_ptm.list[[3]]$ABUNDANCE = y.limup - 1

ptm_temp = .plot.profile.summary.lf(cur_ptm.list, ptm_name,
y.limup, y.limdown, x.axis.size,
y.axis.size, text.size, text.angle, legend.size, dot.size.profile,
ncol.guide)

if (plot_global){
protein_temp = .plot.profile.summary.lf(protein.list, as.character(
plot_proteins[, GLOBALPROTEIN][i]), y.limup, y.limdown, x.axis.size,
y.axis.size, text.size, text.angle, legend.size, dot.size.profile,
cur_protein.list = protein.list
cur_protein.list[[3]]$ABUNDANCE = y.limup - 1
protein_temp = .plot.profile.summary.lf(cur_protein.list, protein_name,
y.limup, y.limdown, x.axis.size,
y.axis.size, text.size, text.angle, legend.size, dot.size.profile,
ncol.guide)
summary_profile_plots <- list(PTEMP.PTM = ptm_temp, PTEMP.PROTEIN = protein_temp)
grid.arrange(ptm_temp, protein_temp, ncol=1)
Expand All @@ -1503,8 +1563,8 @@
print(ptm_temp)
}
output_plots[["summary_plot"]][[paste("plot",i)]] <- summary_profile_plots
message(paste("Drew the Profile plot for ",
as.character(plot_proteins[, PROTEINNAME][i]),
message(paste("Drew the Profile plot for ",
ptm_name,
"(", i, " of ", nrow(plot_proteins), ")"))
}
if (address!=FALSE & !isPlotly) {
Expand Down
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